The following error is shown when I try to knit my r markdown baring in mind all code runs successfully otherwise.
Error in as.ts(x) : object 'Trainingdatar2000_m' not found
Calls: <Anonymous> ... withVisible -> eval -> eval -> acf -> na.action -> as.ts
In addition: Warning messages:
1: In has_crop_tools() :
Tool(s) not installed or not in PATH: pdfcrop, ghostcript
-> As a result, figure cropping will be disabled.
2: In has_crop_tools() :
Tool(s) not installed or not in PATH: pdfcrop, ghostcript
-> As a result, figure cropping will be disabled.
Execution halted```
R Markdown evaluates in its own clean session. Your notebook needs to generate all datasets needed, and will not share objects in the parent session.
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I have been trying to knit I first got an error but then fixed it on the same line. However, I know keep on getting alternative errors, one
Error: package or namespace load failed for ‘vctrs’ in loadNamespace and in 'hevaan'.
And if I am not getting that error I am getting this
Error in contrib.url(repos, "source") :
trying to use CRAN without setting a mirror
Calls: <Anonymous> ... eval_with_user_handlers -> eval -> eval -> install.packages -> contrib.url
Execution halted
However, I fixed these issues with install.packages and it went to 80% of my knit but now it will not go passed 5%.
I am trying to knit and I keep getting this error:
Error in contrib.url(repos, "source") :
trying to use CRAN without setting a mirror
Calls: <Anonymous> ... eval_with_user_handlers -> eval -> eval -> install.packages -> contrib.url
In addition: Warning message:
In eng_r(options) :
Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Execution halted
I tried a 'flexdashboard' themed with 'bslib' (in RStudio: New file -> Rmarkdown -> From template -> flexdashboard themed with bslib). I'm on Windows. When I knit the file (e.g. the default one), the compilation reaches 100% but then an error occurs:
Error in ie_get_proxy_for_url(test_url) :
ERROR_WINHTTP_UNABLE_TO_DOWNLOAD_SCRIPT
Calls : <Anonymous> ... download_file -> <Anonymous> -> ie_get_proxy_for_url
I am trying to create a documentation for my R package using roxygen2, however, when I click to document, I get the following error:
First time using roxygen2. Upgrading automatically...
Error in .f(.x[[i]], ...) : attempt to apply a non-function
Calls: suppressPackageStartupMessages ... read_pkg_description ->
read.description -> <Anonymous> -> .Call -> .f
In an R package, I have a figure (jpeg) located under man/figures, which is added to a Rd file with,
\if{html}{\figure{supplydemand.jpg}{Supply-demand}}
\if{latex}{\figure{supplydemand}{Supply-demand}}
After updating to roxygen2 4.0.1, I get the error:
==> roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace'))
Error in file(con, "r") : cannot open the connection
Calls: suppressPackageStartupMessages ... <Anonymous> -> first_time -> vapply -> FUN -> readLines -> file
In addition: Warning message:
In file(con, "r") : cannot open file './man/figures': Permission denied
Execution halted
Exited with status 1.
If I remove the code to insert the figure, I still get this error. Only when I remove the subdir man/figures does roxygen2 work OK.
I assume this is a bug in roxygen2 or is there a workaround?