Notebook renders differently from document

efg · May 14, 2018, 6:33pm

Why does the same markdown code render quite differently as html_document (OK) and html_notebook (not OK):

output: html_document
RStudio blocked image insert: CRAZY: New users only allowed one image in a post? Why?

output: html_notebook
NotOK

dSample is a SQL Server table reference:

dSample <- tbl(xxx, in_schema("yyy", "zzz"))

jcblum · May 14, 2018, 7:00pm

Is this possibly the same as this issue?

Can you post an image of the html_document output in a separate message? (edited to add: I mean in this thread, not in a new thread, in case that wasn't clear)

(as in so many things on the internet, the reason for limits on new users who are necessarily of as-yet-unknown trustworthiness is that these limits make the site less attractive to abuse by spambots, sock puppets, and trolls )

efg · May 14, 2018, 7:45pm

Thanks jcblum for your quick response. It is possible my problem is the same issue.

I tried to post a .nb.html file with the problem (and planned to post the corresponding .html), but restrictions again: "Sorry, the file you are trying to upload is not authorized (authorized extensions: jpg, jpeg, png, gif, pdf)."

I was able to create a simple example that shows the same problem. (I used dput on the original object that was not displaying correctly).

y <- structure(list(n = 768L), row.names = c(NA, -1L), class = c("tbl_df", 
"tbl", "data.frame"))

y does not display correctly in a notebook, but looks fine in a document.

It's possible this problem is related to the new R 3.5.0.

I'm not seeing the same problem with R 3.4.4 on a different machine. (When I tried to reconfigure RStudio to use R 3.4.4, which is still present, I get an error that appears to be connected to the Rcpp.dll.)

jcblum · May 14, 2018, 8:20pm

Just to clarify, how does y display in an nb.html viewed in a web browser?

If it is the same bug, it looks like there may have been some progress in recent dailies, if you're up for trying that. See here:

github.com/rstudio/rstudio

attempts to print tbl_dfs as paged tables in Notebooks fail with R 3.5.

opened 08:41PM - 05 May 18 UTC

closed 11:22PM - 09 May 18 UTC

kevinushey

bug

### System details RStudio Edition : Desktop RStudio Version : v1.2.…602 OS Version : macOS 10.13.4 R Version : 3.5.0 ### Steps to reproduce the problem Try running the following chunk in an R Notebook: ```R library(tibble) as_tibble(mtcars) ``` ### Describe the problem in detail The table is printed as 'plain' `tibble` output, rather than as a paged table. ### Describe the behavior you expected This should be printed as a paged table. ### Diagnosis From https://github.com/rstudio/rmarkdown/issues/1331: Something appears to be going awry with S3 dispatch in the Notebook context. One can see the issue by attempting to debug the `print` call in a Notebook chunk, using R 3.5.0 with RStudio v1.2: ````` ```{r} debugonce(print) as_tibble(mtcars) ``` ````` When running this, I see: ```R > debugonce(print) > as_tibble(mtcars) debugging in: function (x, ...) UseMethod("print")(x) debug: UseMethod("print") Browse[2]> class(x) [1] "tbl_df" "tbl" "data.frame" Browse[2]> print.tbl_df function (x, ...) { o <- overrideMap(x, options) if (!is.null(o)) { overridePrint(o$x, o$options, o$className, o$nRow, o$nCol) } } <bytecode: 0x7fad5be20ec0> <environment: 0x7fad44a37498> ``` So it appears like the S3 override we've registered should be in scope for this print call. However, this is not the case -- the S3 method registered in `tibble` is called instead. ```R Browse[2]> s debugging in: print.tbl_df(x) debug: { cat_line(format(x, ..., n = n, width = width, n_extra = n_extra)) invisible(x) } ``` The [NEWS](https://cran.r-project.org/doc/manuals/r-release/NEWS.html) file of R 3.5.0 has this: > - S3 method lookup now searches the namespace registry after the top level environment of the calling environment. So it seems like R has explicitly switched up the mechanism used for S3 dispatch, and this has broken the way we override the S3 methods when injecting our own printers. We'll have to think about how to accommodate this change in behavior.

efg · May 14, 2018, 8:29pm

The output for y appears exactly like the output I originally posted -- the line that starts "[38;5;246m# A tibble ..." Chrome and RStudio display the same thing.

Thanks the info about the daily builds. I need a stable fix. I may downgrade to R 3.4.4.

I'll be more cautious about upgrades next time.

jcblum · May 14, 2018, 8:46pm

Sadly, sometimes downgrading is the shortest path back to getting work done... Good luck!

kevinushey · May 14, 2018, 10:03pm

For what it's worth, we do plan on producing a patch release of the v1.1 branch with a fix for the issue you've encountered, and that should hopefully be published soon (hopefully by the end of this week). Sorry for the trouble!

efg · May 22, 2018, 8:44pm

I installed RStudio 1.1.453 released 2018-05-16 and I don't see the problem. Thanks!