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.
Related
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 getting an error message while running knit to HTML. But If I run chunk individually, it draws plot as expected.
What would be a problem? The error message is below:
Quitting from lines 270-274 (HC_FC_indivisual_cellline_fdr_1%.Rmd)
Error in png(..., res = dpi, units = "in") : invalid 'filename' Calls:
... in_dir -> plot2dev -> do.call -> -> png
Execution halted
The described error also occurs, when you are knitting plots within named code chunks, and the name of the chunk does not lead to a valid path name during knitting process.
That is, during the knitting process the plots are written into a temporary path which contains the name of the code chunk, ergo this name should contain only characters that are valid for path names. One should avoid to use white characters for chunk names as well.
I ran into the same issue. I ran this right before my first plot in the chunk and it solved it for me
dev.off()
hope this helps.
I had the same problem. I updated R to the latest version and also RStudio. Install the required packages for the knit and then everything became fine.
Adding 'dev.off()' can solve the problem for knitting but will cause another problem and does not show the plots in the HTML file.
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?
I am just starting to explore the rmarkdown package. I don't use Rstudio. I use the default R environment. What I did was as follows.
I created a new R document.
Started typing few lines in rmarkdown format.
Saved the file with Rmd extension.
I saved the file in the working directory.
I installed the pandoc using the pkg file.
I installed 'rmarkdown' package. Loaded the package.
Used the following command to render the Rmd file.
rmarkdown::render("Untitled.Rmd")
I get the following error.
Error in tools::file_path_as_absolute(input) : file 'Untitled.Rmd'
does not exist
I tried all the possible ways such as giving the exact path instead of filename etc. But nothing worked out. I googled the error message and found that none had similar error. Can someone help me with this. What I am missing. What the error message mean?
Most of the time the error file not found is either a type error or a real missing file (as in your case, the real one is named in another way).
In order to discard those possibilities:
Copy the fullpath from your filebrowser.
Make sure the file exists, inside R you could type:
file.exists("/fullpath/to/file")
If that return TRUE and the error persists, then you suspect another thing is going on.