kableExtra
kableExtra copied to clipboard
haozhu233
column_spec give error: Error in UseMethod("nodeset_apply") : no applicable method for 'nodeset_apply' applied to an object of class "NULL"
I have a data table I want to display for HTML report
BelQ= structure(list(Source = "Kalender 2019", `Sourse of Questions` = "The survey instruments were part of a larger survey that included other motivational constructs. The development and validation of these surveys is reported in prior work [18–22,59]. ", Results = "PCA analysis reveals that for both genders, sense of belonging and identity were not separate from the Expectancy Value Theory constructs. Instead, sense of belonging was closely tied to self-efficacy, which was therefore labeled as “self-efficacy or belonging” component or factor. ", Questions = "Sense of Belonging or Self-efficacy (not separated in a paper):<br>1. Sometimes I worry that I do not belong in this physics class<br>2. I feel like I can be myself in this class<br>3. I am able to help my classmates with physics in the laboratory or in recitation<br>4. I understand concepts I have studied in physics<br>5. If I wanted to, I could be good at physics research<br>6. ", Reference = "Kalender, Z. Y., Marshman, E., Schunn, C. D., Nokes-Malach, T. J., & Singh, C. (2019). Gendered patterns in the construction of physics identity from motivational factors. Physical Review Physics Education Research, 15(2), [020119](https://journals.aps.org/prper/abstract/10.1103/PhysRevPhysEducRes.15.020119)"), row.names = c(NA, -1L), class = c("tbl_df", "tbl", "data.frame"))
when I try to produce a table I am not able to change teh widths of teh columns and I get teh error Error in UseMethod("nodeset_apply") : no applicable method for 'nodeset_apply' applied to an object of class "NULL"
BelQ %>% kbl() %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed"),font_size = 12, full_width = T) %>%
kableExtra::scroll_box(width = "100%", height = "500px") %>%
column_spec(1, width = "40em", include_thead=T)
I usually just use scroll_box at the very end. In your case, just flip the order of these two function will do the trick
... %>%
column_spec(1, width = "40em", include_thead=T) %>%
kableExtra::scroll_box(width = "100%", height = "500px")
I have installed the development version and I get the exact same error, no mater the order of the commands. I also get it with other commands when using include_thead=T.
Oh, yeah, I think I probably broke it in a recent commit. I will look into it.
Hello haozhu, could you give us an update please? I installed recent version and the problem persists.
Thank you
Hello - I wanted to check in on this as well. Do you expect a fix or have a suggestion as to how to fix this?
column_spec() seems to be broken. I can't change the font_size by column, for example.
In my case , i find the error:
column_spec give error: Error in UseMethod("nodeset_apply") : no applicable method for 'nodeset_apply' applied to an object of class "NULL"
not when I knit the document, but when I loop-knit it , using parameters.
Wanted to check if we can expect a fix or if there is a known workaround? I'm getting the same error when using include_thead = T
I'm getting the same errors. I was able to convince it to knit, but it used 100+% of CPU for a few minutes and crashed RStudio. column_spec() works for me in other code blocks and documents, it seems that only in combination with scroll_box() does it become unstable.
The commented line - https://github.com/haozhu233/kableExtra/commit/6fc251d1f66ae97adbda913bd7b6fe6e10751be8 is causing this I think
The problem seems to be that this offset is set to 1 for include_thead = TRUE which means the for loop reads beyond the end of the rows.
I'm not entirely sure what the existing code is trying to do - it's not obvious to me what is happening inside the include_thead branch - apologies for this - coming at it cold...
It looks like it should be easy to avoid the row overflow - e.g. just by changing the iteration sequence to something like for (io in seq(off + 1, length(all_contents_rows))) but I'm not actually sure if that leaves an underlying issue - is there something else going on with the rows here (should one be added?)
I'll go read the documentation....
OK - think I can see what is happening now.
I'm afraid I haven't tested this in anger... but I have debugged through my local issue - think using i for body row columns and io for the format properties should work 👍 https://github.com/haozhu233/kableExtra/pull/646
I've run into this issue as well, and can confirm that @slodge's PR https://github.com/haozhu233/kableExtra/pull/646 fixes the error.
Bumping up that there is a PR here that seems to fix the issue but it hasn't been merged.
Same:
library(magrittr)
cars %>%
knitr::kable() %>%
kableExtra::column_spec(1,
include_thead = TRUE, # works for FALSE
background = "red")
#> Error in UseMethod("nodeset_apply"): no applicable method for 'nodeset_apply' applied to an object of class "NULL"
Created on 2022-08-31 by the reprex package (v2.0.1)
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.1.2 (2021-11-01)
#> os macOS Big Sur 10.16
#> system x86_64, darwin17.0
#> ui X11
#> language (EN)
#> collate en_AU.UTF-8
#> ctype en_AU.UTF-8
#> tz Australia/Melbourne
#> date 2022-08-31
#> pandoc 2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.0)
#> cli 3.3.0 2022-04-25 [1] CRAN (R 4.1.2)
#> colorspace 2.0-3 2022-02-19 [1] R-Forge (R 4.1.2)
#> digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.0)
#> evaluate 0.15 2022-02-18 [1] CRAN (R 4.1.2)
#> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.1.2)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0)
#> fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.0)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.2)
#> highr 0.9 2021-04-16 [1] CRAN (R 4.1.0)
#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.1.2)
#> httr 1.4.3 2022-05-04 [1] CRAN (R 4.1.2)
#> kableExtra 1.3.4 2021-02-20 [1] CRAN (R 4.1.2)
#> knitr 1.39 2022-04-26 [1] CRAN (R 4.1.2)
#> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.0)
#> magrittr * 2.0.3 2022-03-30 [1] CRAN (R 4.1.2)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
#> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.1.2)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
#> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
#> R.cache 0.15.0 2021-04-30 [1] CRAN (R 4.1.0)
#> R.methodsS3 1.8.1 2020-08-26 [1] CRAN (R 4.1.0)
#> R.oo 1.24.0 2020-08-26 [1] CRAN (R 4.1.0)
#> R.utils 2.11.0 2021-09-26 [1] CRAN (R 4.1.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0)
#> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.0)
#> rlang 1.0.4 2022-07-12 [1] CRAN (R 4.1.2)
#> rmarkdown 2.14 2022-04-25 [1] CRAN (R 4.1.2)
#> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
#> rvest 1.0.2 2021-10-16 [1] CRAN (R 4.1.0)
#> scales 1.2.1 2022-08-20 [1] CRAN (R 4.1.2)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.0)
#> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.1.2)
#> stringr 1.4.1 2022-08-20 [1] CRAN (R 4.1.2)
#> styler 1.6.2 2021-09-23 [1] CRAN (R 4.1.0)
#> svglite 2.0.0 2021-02-20 [1] CRAN (R 4.1.0)
#> systemfonts 1.0.3 2021-10-13 [1] CRAN (R 4.1.2)
#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.1.2)
#> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0)
#> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.1.2)
#> viridisLite 0.4.1 2022-08-22 [1] CRAN (R 4.1.2)
#> webshot 0.5.3 2022-04-14 [1] CRAN (R 4.1.2)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.2)
#> xfun 0.31 2022-05-10 [1] CRAN (R 4.1.2)
#> xml2 1.3.3 2021-11-30 [1] CRAN (R 4.1.0)
#> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.1.2)
#>
#> [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
I just hit this same error again... over a year after the PR with a fix...
Is this project still alive? Do you need anyone else to assist?
did you tried their new function kbl() instead of kable() (https://cran.r-project.org/web/packages/kableExtra/vignettes/awesome_table_in_html.html)? may be it is resolved there?
@yuliaUU like this?
> cars %>%
+ kableExtra::kbl() %>%
+ kableExtra::column_spec(1,
+ include_thead = TRUE, # works for FALSE
+ background = "red")
Error in UseMethod("nodeset_apply") :
no applicable method for 'nodeset_apply' applied to an object of class "NULL"
I was the one who submitted the #646 PR - it's a one character fix, but took some digging to find... it's a shame that it continues to cause pain :/
If anyone wants a single code file to source in their app/report/script then this works as long as you call it after library(kableExtra)
# THIS FILE BASED FROM https://raw.githubusercontent.com/slodge/kableExtra/master/R/column_spec.R
# See https://github.com/haozhu233/kableExtra/pull/646 (open >1 year currently)
#' Specify the look of the selected column
#'
#' @description This function allows users to select a column and then specify
#' its look.
#'
#' @param kable_input Output of `knitr::kable()` with `format` specified
#' @param column A numeric value or vector indicating which column(s) to be selected.
#' @param width A character string telling HTML & LaTeX how wide the column
#' needs to be, e.g. "10cm", "3in" or "30em".
#' @param bold T/F value or vector to control whether the text of the selected
#' column need to be bolded.
#' @param italic T/F value or vector to control whether the text of the
#' selected column need to be emphasized.
#' @param monospace T/F value or vector to control whether the text of the
#' selected column need to be monospaced (verbatim)
#' @param underline T/F value or vector to control whether the text of the
#' selected row need to be underlined
#' @param strikeout T/F value or vector to control whether the text of the
#' selected row need to be striked out.
#' @param color A character string or vector for column text color. Here please
#' pay attention to the differences in color codes between HTML and LaTeX.
#' @param background A character string or vector for column background color. Here please
#' pay attention to the differences in color codes between HTML and LaTeX.
#' @param border_left A logical variable indicating whether there should be a
#' border line on the left of the selected column. In HTML, you can also pass
#' in a character string for the CSS of the border line
#' @param border_right A logical variable indicating whether there should be a
#' border line on the right of the selected column. In HTML, you can also pass
#' in a character string for the CSS of the border line
#' @param width_min Only for HTML table. Normal column width will automatically
#' collapse when the window cannot hold enough contents. With this `width_min`,
#' you can set up a column with a width that won't collapse even when the
#' window is not wide enough.
#' @param width_max Only for HTML table. `width_max` defines the maximum width
#' of table columns.
#' @param extra_css A vector of extra css text to be passed into the cells of
#' the column.
#' @param include_thead T/F. A HTML only feature to contoll whether the
#' header row will be manipulated. Default is `FALSE`.
#' @param latex_column_spec Only for LaTeX tables. Code to replace the column
#' specification. If not `NULL`, will override all other arguments.
#' @param latex_valign vertical alignment. Only works when you specified column
#' width. Choose among `p`, `m`, `b`.
#' @param link A vector of strings for url links.
#' @param new_tab T/F for whether to open up the new link in new tab
#' @param tooltip A vector of strings to be displayed as tooltip.
#' Obviously, this feature is only available in HTML. Read the package
#' vignette to see how to use bootstrap tooltip css to improve the loading
#' speed and look.
#' @param popover Similar with tooltip but can hold more contents. The best way
#' to build a popover is through `spec_popover()`. If you only provide a text
#' string, it will be used as content. Note that You have to enable this
#' bootstrap module manually. Read the package vignette to see how.
#' @param image Vector of image paths.
#'
#' @details Use `latex_column_spec` in a LaTeX table to change or
#' customize the column specification. Because of the way it is handled
#' internally, any backslashes must be escaped.
#'
#' @examples
#' \dontrun{
#' x <- knitr::kable(head(mtcars), "html")
#' column_spec(x, 1:2, width = "20em", bold = TRUE, italic = TRUE)
#' x <- knitr::kable(head(mtcars), "latex", booktabs = TRUE)
#' column_spec(x, 1, latex_column_spec = ">{\\\\color{red}}c")
#' }
#' @export
column_spec <- function(kable_input, column,
width = NULL, bold = FALSE, italic = FALSE,
monospace = FALSE, underline = FALSE, strikeout = FALSE,
color = NULL, background = NULL,
border_left = FALSE, border_right = FALSE,
width_min = NULL, width_max = NULL,
extra_css = NULL, include_thead = FALSE,
latex_column_spec = NULL, latex_valign = 'p',
link = NULL, new_tab = TRUE,
tooltip = NULL, popover = NULL, image = NULL) {
if (!is.numeric(column)) {
stop("column must be numeric. ")
}
kable_format <- attr(kable_input, "format")
if (!kable_format %in% c("html", "latex")) {
warning("Please specify format in kable. kableExtra can customize either ",
"HTML or LaTeX outputs. See https://haozhu233.github.io/kableExtra/ ",
"for details.")
return(kable_input)
}
if (kable_format == "html") {
return(kabelcolumn_spec_html_hacked(kable_input, column, width,
bold, italic, monospace,
underline, strikeout,
color, background,
border_left, border_right,
width_min, width_max,
extra_css, include_thead,
link, new_tab, tooltip, popover, image))
}
if (kable_format == "latex") {
return(kableExtra:::column_spec_latex(kable_input, column, width,
bold, italic, monospace,
underline, strikeout,
color, background,
border_left, border_right,
latex_column_spec, latex_valign, include_thead,
link, image))
}
}
kabelcolumn_spec_html_hacked <- function(kable_input, column, width,
bold, italic, monospace,
underline, strikeout,
color, background,
border_left, border_right,
width_min, width_max,
extra_css, include_thead,
link, new_tab, tooltip, popover, image) {
kable_attrs <- attributes(kable_input)
kable_xml <- kableExtra:::kable_as_xml(kable_input)
kable_tbody <- kableExtra:::xml_tpart(kable_xml, "tbody")
group_header_rows <- attr(kable_input, "group_header_rows")
all_contents_rows <- seq(1, length(xml2::xml_children(kable_tbody)))
if (!is.null(group_header_rows)) {
all_contents_rows <- all_contents_rows[!all_contents_rows %in%
group_header_rows]
}
# Border css
border_l_css <- "1px solid"
border_r_css <- "1px solid"
if (is.character(border_left)) {
border_l_css <- border_left
border_left <- T
}
if (is.character(border_right)) {
border_r_css <- border_right
border_right <- T
}
if (include_thead) {
nrows <- length(all_contents_rows) + 1
off <- 1
bold <- kableExtra:::ensure_len_html(bold, nrows, "bold")
italic <- kableExtra:::ensure_len_html(italic, nrows, "italic")
monospace <- kableExtra:::ensure_len_html(monospace, nrows, "monospace")
underline <- kableExtra:::ensure_len_html(underline, nrows, "underline")
strikeout <- kableExtra:::ensure_len_html(strikeout, nrows, "strikeout")
color <- kableExtra:::ensure_len_html(color, nrows, "color")
background <- kableExtra:::ensure_len_html(background, nrows,"background")
link <- kableExtra:::ensure_len_html(link, nrows, "link")
new_tab <- kableExtra:::ensure_len_html(new_tab, nrows, "new_tab")
tooltip <- kableExtra:::ensure_len_html(tooltip, nrows, "tooltip")
popover <- kableExtra:::ensure_len_html(popover, nrows, "popover")
image <- kableExtra:::ensure_len_html(image, nrows, "image")
kable_thead <- kableExtra:::xml_tpart(kable_xml, "thead")
nrow_thead <- length(xml2::xml_children(kable_thead))
for (j in column) {
target_cell <- xml2::xml_child(xml2::xml_child(kable_thead, nrow_thead), j)
kableExtra:::column_spec_html_cell(
target_cell, width, width_min, width_max,
bold[1], italic[1], monospace[1], underline[1], strikeout[1],
color[1], background[1], border_left, border_right,
border_l_css, border_r_css,
extra_css,
link[1], new_tab[1], tooltip[1], popover[1], image[1]
)
}
} else {
nrows <- length(all_contents_rows)
off <- 0
bold <- kableExtra:::ensure_len_html(bold, nrows, "bold")
italic <- kableExtra:::ensure_len_html(italic, nrows, "italic")
monospace <- kableExtra:::ensure_len_html(monospace, nrows, "monospace")
underline <- kableExtra:::ensure_len_html(underline, nrows, "underline")
strikeout <- kableExtra:::ensure_len_html(strikeout, nrows, "strikeout")
color <- kableExtra:::ensure_len_html(color, nrows, "color")
background <- kableExtra:::ensure_len_html(background, nrows,"background")
link <- kableExtra:::ensure_len_html(link, nrows, "link")
new_tab <- kableExtra:::ensure_len_html(new_tab, nrows, "new_tab")
tooltip <- kableExtra:::ensure_len_html(tooltip, nrows, "tooltip")
popover <- kableExtra:::ensure_len_html(popover, nrows, "popover")
image <- kableExtra:::ensure_len_html(image, nrows, "image")
}
for (i in seq(length(all_contents_rows))) {
for (j in column) {
io <- i + off
target_cell <- xml2::xml_child(xml2::xml_child(kable_tbody, all_contents_rows[i]), j)
kableExtra:::column_spec_html_cell(
target_cell, width, width_min, width_max,
bold[io], italic[io], monospace[io], underline[io], strikeout[io],
color[io], background[io], border_left, border_right,
border_l_css, border_r_css,
extra_css,
link[io], new_tab[io], tooltip[io], popover[io], image[io]
)
}
}
out <- kableExtra:::as_kable_xml(kable_xml)
attributes(out) <- kable_attrs
if (!"kableExtra" %in% class(out)) class(out) <- c("kableExtra", class(out))
return(out)
}
