I'm using xlsx to read from my Excel files (actually OpenOffice, saved as .xls) with the read.xlsx function.
It's working perfectly fine in .R scripts, and it runs perfectly fine in .Rmd code chunks. But then when I try to make a pdf/html/whatever using knitr, I get:
Error in eval(expr, envir, enclos) : could not find function "read.xlsx"
Calls: ... handle -> withCallingHandlers -> withVisible -> eval -> eval
Help? How can it not find a function it has already used in the same .Rmd file?
Related
I am trying to compile a pdf report of my R code. I imported the dataset using the menu options but am now having trouble compiling it because R cannot find the .csv files I used. I have triple checked and the working directory is correct.
I get this error:
Error in eval(expr, envir, enclos) : object 'filename' not found
Calls: <Anonymous>...withVisible...-> eval with Userhandlers -> eval -> eval
Execution Halted
Would appreciate any help. Thanks!
Tried getwd() and setwd() but that doesn't seem to be the issue. Double checked file names and location.
Are you trying to compile an RMarkdown file to pdf? If so, you can specify the working directory in the beginning like this:
knitr::opts_knit$set(root.dir = '/tmp')
At any rate, it should also work if you use the full path name as filename.
When I'm knitting my r markdown document it all runs smoothly until 1 chunk near the end where I get the error in the render tab (near where the console is):
error pic
I'll write down what the code says just in case the image doesn't load:
Quitting from lines 1321-1372 (narrative_analysis2.Rmd)
Error in app$vspace(new_style$`margin-top` %||% 0) :
attempt to apply non-function
Calls: <Anonymous> ... <Anonymous> -> .transformer -> clii__container_start
Execution halted
Lines 1321 - 1372 are in a specific chunk where no errors come up when I run that specific chunk. I uploaded my excel data through readxl package. The chunk before and the chunk after all run smoothly. I don't know what is the issue. narrative_analysis2 is the name I saved the markdown as.
I have reinstalled knitr, readr, readxl, cli and restarted the session and nothing has worked. I don't understand why it won't knit.
Does anyone have any advice?
Hello StackOverflow community,
I have been trying over the last few weeks using R Markdown to Knit HTML file.
While it use to run smoothly the previous time, over the last week I keep on getting the following error
Quitting from lines 43-92 (Vizualisation.Rmd)
Error in eval(lhs, parent, parent) :
object 'processed.feedback' not found
Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> %>% -> eval -> eval
Execution halted
The thing is that my source 'processed.feedback' is loaded within my Global environment. But is not created with the .rmd but before in a script file.
If I do the wrangling as well in the same Rmarkdown the it works fine (no error). But I would love to keep the wrangling part in a separate file.
Any suggestion.
Thanks in advance for your feedback and help!
If you are at the Rstudio conference - enjoy!
The usual model is that R Markdown files do not see objects that are in your workspace: they start with a blank workspace, so that anyone can reproduce the computation. (There are ways to work in an existing workspace, but you shouldn't use them.)
If it takes too long to create an object in the Rmd code, then there are at least two options: turn on caching (so it only happens when necessary), or save the object in a separate file using save() and load it in your document using load(). Remember to distribute the save file along with the .Rmd file if you want to give this document to someone else.
I'm trying to create a PDF in R Markdown and I keep getting this error message every time I try to click "Knit to PDF":
output file: test_4_for_r.knit.md
Output created: test_4_for_r.pdf
Error in tools::file_path_as_absolute(output_file) :
file 'test_4_for_r.pdf' does not exist
Calls: <Anonymous> -> <Anonymous>
In addition: Warning message:
In readLines(logfile) : incomplete final line found on 'test_4_for_r.log'
Execution halted
I do not have a lot of familiarity with RStudio, so I have no idea why I'm getting this message. I've read several things online saying creating PDFs in R Markdown requires several packages, but so far I've only found the name of knitr. That is the only one I have currently installed. I'm not sure if that is the issue or not.
Can someone please point me in the right direction on how to remedy this? Any help would be GREATLY appreciated.
In R-Studio Tools > Global Options, under the Sweave tab, try changing "Weave Rnw using:" from sweave to knitr. Also try
install.packages('tinytex')
tinytex::install_tinytex()
and then try to knit your PDF.
If those don't work, please paste the markdown code giving you trouble. Could you knit the example markdown file, found when you File > New File > R Markdown?
I am creating an R package, and have a graph.rda file inside my data folder.
In RStudio in the .rmd vignette file, I read the data in:
data(graph)
head(graph)
but when I "Knit HTML" the .rmd vignette file, I get an error on these above two lines saying:
"Error in head(sbTree): object 'sbTree' not found Calls:
<Anonymous> ... withCallingHandlers -> withVisible ->
eval -> eval -> head Execution halted"
I have tried researching for solutions and tried some of the suggestions (like adding library(knitr)), but to no avail.
Any advice is greatly appreciated!