Error in Regexpr: Unable to find current file

[tford9]

While attempting to Knit a markdown file I'm receiving this error:

[randy3k]

How about running it via terminal or R?

Could you share your Rmarkdown file or provide a minimal example file?

[lf-araujo]

I can confirm this issue on Windows, my entire error reads:

Error in regexpr("\\.([[:alnum:]]+)$", x) : object 'teste.Rmd' not found
Calls: <Anonymous> -> %in% -> tolower -> <Anonymous> -> regexpr
Execution halted
[Finished in 0.8s with exit code 1]
[cmd: ['C:\\Users\\luis.araujo\\Documents\\R\\R-3.5.1\\bin\\x64\\R.exe', '--slave', '-e', 'rmarkdown::render("teste.Rmd", encoding = "UTF-8")']]
[dir: C:\Users\luis.araujo\Downloads]
[path: C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Users\luis.araujo\AppData\Local\Microsoft\WindowsApps;C:\Users\luis.araujo\AppData\Local\Programs\Git\cmd;C:\Users\luis.araujo\AppData\Local\Pandoc\;C:\Users\luis.araujo\Documents\R\R-3.5.1\bin\x64]

I can´t figure out what is going on here. As per your question to @tford9 it works as expected on Terminus:

> rmarkdown::render("teste.Rmd", encoding = "UTF-8")                                    

processing file: teste.Rmd                                                              
  |.................................................................| 100%              
  ordinary text without R code                                                          

output file: teste.knit.md                                                              

"C:/Users/LUIS~1.ARA/AppData/Local/Pandoc/pandoc" +RTS -K512m -RTS teste.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output teste.html --email-obfuscation none --self-contained --standalone --section-divs --template "C:\Users\luis.araujo\Documents\R\R-3.5.1\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable "theme:bootstrap" --include-in-header "C:\Users\LUIS~1.ARA\AppData\Local\Temp\Rtmp8swhBi\rmarkdown-str126867b33c9c.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --metadata pagetitle=teste.utf8.md                              

Output created: teste.html   

For contents:

# Title

Contents.

[lf-araujo]

@tford9 were you able to find a solution to this?

[randy3k]

@lf-araujo is file located at C:\Users\luis.araujo\Downloads\teste.Rmd?

[lf-araujo]

I just recreated it at that folder, error persists as previous post. The folder it is saved in does not matter, as it will fail on Windows. R-ide works perfectly on Ubuntu, so it seems to be system specific.

[lf-araujo]

I think this is the class responsible for running render, it seems ok, I can´t identify the problem:

class RideRenderRmarkdownCommand(sublime_plugin.WindowCommand):
    def is_enabled(self):
        view = self.window.active_view()
        return view.settings().get("syntax").endswith("R Markdown.sublime-syntax")

    def run(self, kill=False):
        cmd = "rmarkdown::render(\"$file_name\", encoding = \"UTF-8\")"
        cmd = sublime.expand_variables(cmd, self.window.extract_variables())
        kwargs = {}
        kwargs["cmd"] = [ride_settings.r_binary(), "--slave", "-e", cmd]
        kwargs["working_dir"] = os.path.dirname(self.window.active_view().file_name())
        kwargs["env"] = {
            "PATH": ride_settings.custom_env("PATH"),
            "LANG": ride_settings.get("lang", "en_US.UTF-8")
        }
        kwargs["kill"] = kill
        self.window.run_command("exec", kwargs)

• Is it perhaps related to the way sublimetext expands the filenames?

[randy3k]

It seems to me that Sublime Text is treating the command as

rmarkdown::render(teste.Rmd, encoding = UTF-8)

without the quotations, that's why the object teste.Rmd was not found.

[lf-araujo]

Yep, this is what it looks like.

I tried to use $file or wrap that section in single quotes to no avail.

I am beginning to think the problem is in Sublime.

[randy3k]

It seems that single quotes would work.

[lf-araujo]

I think this is related to how sublime text expands file paths in windows, is there some property that I can pass to the python library to signal that the command should be run in a windows environment?

The error I get when I run it with single quotes is:

Error: '\P' is an unrecognized escape in character string starting "'Y:\P"
Execution halted
[Finished in 2.6s]

Because the path is something like Y:\Projects\data

[randy3k]

But '$file_name' should be just the file name without the folder.

[lf-araujo]

It solves the problem, I must have it set to $file at some point. It is now working normally under Windows.

Can I ask you randy, how you inspect the objects in memory while working with R?

I use a small function I found on SO, which lists the objects and their size in memory:

# improved list of objects
.ls.objects <- function (pos = 1, pattern, order.by,
                        decreasing=FALSE, head=FALSE, n=5) {
    napply <- function(names, fn) sapply(names, function(x)
                                         fn(get(x, pos = pos)))
    names <- ls(pos = pos, pattern = pattern)
    obj.class <- napply(names, function(x) as.character(class(x))[1])
    obj.mode <- napply(names, mode)
    obj.type <- ifelse(is.na(obj.class), obj.mode, obj.class)
    obj.prettysize <- napply(names, function(x) {
                           format(utils::object.size(x), units = "auto") })
    obj.size <- napply(names, object.size)
    obj.dim <- t(napply(names, function(x)
                        as.numeric(dim(x))[1:2]))
    vec <- is.na(obj.dim)[, 1] & (obj.type != "function")
    obj.dim[vec, 1] <- napply(names, length)[vec]
    out <- data.frame(obj.type, obj.size, obj.prettysize, obj.dim)
    names(out) <- c("Type", "Size", "PrettySize", "Length/Rows", "Columns")
    if (!missing(order.by))
        out <- out[order(out[[order.by]], decreasing=decreasing), ]
    if (head)
        out <- head(out, n)
    out
}
# shorthand
lsos <- function(..., n=10) {
    .ls.objects(..., order.by="Size", decreasing=TRUE, head=TRUE, n=n)
}

Which looks like:

> lsos()
                   Type      Size PrettySize Length/Rows Columns            
elders       data.table 729451712   695.7 Mb     2893779      47            
in.f         data.frame    473696   462.6 Kb        1833      45            
a             character      4888     4.8 Kb           1      NA            
project.info       list      3008     2.9 Kb           1      NA            
config             list      2728     2.7 Kb          16      NA            
schedule      character       888  888 bytes           1      NA    

• Do you have a more efficient way of listing and accessing R objects in memory?

[randy3k]

I am not sure what you want to achieve, but there is https://www.rdocumentation.org/packages/pryr/versions/0.1.4/topics/object_size which is not more robust.

[lf-araujo]

What I want is a simple way of reproducing an Environment panel from RStudio, using r-ide:

[randy3k]

I see. It's going to be a difficult task.

[katrinleinweber]

[...] single quotes would work

and

[...] '$file_name' should be just the file name without the folder.

solved this problem for me as well, also when not using REditorSupport, but Git Bash and (a) make(file) on Windows:

README=README.Rmd

README.md: ${README}
    Rscript -e "rmarkdown::render('$<')"

Thank you so much for sharing this error and its solution, @randy3k & @tford9 :-)

[DSqiansun]

Hello,

I know this ticket id closed. But I got the same issus. I found this: rmarkdown::render('teste.Rmd', encoding = 'UTF-8') Rscript -e "rmarkdown::render('teste.Rmd', encoding = 'UTF-8')"