R sweave writes connection closed warning message on PDF output

Question

I am producing iteratively thousands of PDF reports based on a .Rnw template. The charts I include are pre-generated as .png, not generated on the fly.

My issue is that about 1% of the times (I haven´t found a pattern so far), I get a very visible pink warning message:

## Warning: cerrando la conenexion 3 (report.Rnw) que no esta siendo utilizada

The R code I use to generate the PDF from Sweave is:

Sweave2knitr(file = "report.Rnw",
             output = "./temp/report-knitr.Rnw")
knit2pdf(input = "./temp/report-knitr.Rnw",
         quiet = TRUE,
         clean = TRUE,
         envir = environment(),
         encoding = "UTF-8")

Additionally, I use the library kableExtra to generate tables and xelatex.

Apparently, regenerating the file makes the message go away, so I use the package pdftools to open each report and check for error messages, but I am still concerned and curious about why I get the message, for I don't open explicitly any connection in my scripts, so a part of R/LaTeX compiler must be doing it.

How can I control that my scripts don't leave any connections open?

Answer 1

There's a bug in Sweave2knitr(). It opens a connection to the source file and never closes it. The connection will be closed at the next garbage collection, which can happen at fairly unpredictable times.

So to fix this, don't call Sweave2knitr() so many times (as I suggested in my comment), or call gc() afterwards to generate the warning before calling knit2pdf(). That might slow things down, but probably not noticeably, since knit2pdf is likely pretty slow.