CODEWITHSUNDEEP
rknitrr-markdownboxplot
Krug
Krug

Reputation: 1013

Knit HTML fails to output upon code error

My R script creates a series of matrices and boxplots of those matrixes. It is possible that one of the matrices may be empty. Executing boxplot of an empty matrix gives an error. That is not a problem. The problem is, when running this code in R Markdown to knit an HTML file, this error halts the execution and results in no HTML file.

As a patch, I though to run boxplot only if the matrix is not all NAs. That works. Yet I'd like to know if I could get knitr to simply ignore this error, rather than patch my code. Thank you.

This is the error message:

Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars$yaxs) : 
  need finite 'ylim' values
Calls: <Anonymous> ... boxplot -> boxplot.default -> do.call -> bxp -> plot.window
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
Execution halted

Reproducible code:

```{r,echo = FALSE, warning = FALSE, message=FALSE}
knitr::opts_chunk$set(cache=TRUE)

#MatrixPos - not empty
MatrixPos <- structure(list(difFwd1 = 0, difFwd2 = 0.200000000000045, difFwd3 = 0.100000000000136,difFwd4 = 0, difFwd5 = 0.200000000000045), .Names = c("difFwd1","difFwd2", "difFwd3", "difFwd4", "difFwd5"), row.names = "155", class = "data.frame") 

#MatrixNeg - empty
MatrixNeg <- structure(list(difFwd1 = NA_real_, difFwd2 = NA_real_, difFwd3 = NA_real_,difFwd4 = NA_real_, difFwd5 = NA_real_), .Names = c("difFwd1","difFwd2", "difFwd3", "difFwd4", "difFwd5"), row.names = "NA", class = "data.frame") 

boxplot(MatrixPos, notch = TRUE, outline = TRUE)
boxplot(MatrixNeg, notch = TRUE, outline = TRUE)

```
###note must remove the four spaces for the code to work in R-Studio


#Solution attempt:
if(!all(is.na(MatrixNeg))) boxplot(MatrixNeg, notch = TRUE, outline = TRUE)

Upvotes: 3

Views: 1500

Answers (1)

ano
ano

Reputation: 704

Try setting error=TRUE in your chunk options

```{r,echo = FALSE, warning = FALSE, message=FALSE, error=TRUE}
knitr::opts_chunk$set(cache=TRUE)

#MatrixPos - not empty
MatrixPos <- structure(list(difFwd1 = 0, difFwd2 = 0.200000000000045, difFwd3 = 0.100000000000136,difFwd4 = 0, difFwd5 = 0.200000000000045), .Names = c("difFwd1","difFwd2", "difFwd3", "difFwd4", "difFwd5"), row.names = "155", class = "data.frame") 

#MatrixNeg - empty
MatrixNeg <- structure(list(difFwd1 = NA_real_, difFwd2 = NA_real_, difFwd3 = NA_real_,difFwd4 = NA_real_, difFwd5 = NA_real_), .Names = c("difFwd1","difFwd2", "difFwd3", "difFwd4", "difFwd5"), row.names = "NA", class = "data.frame") 

boxplot(MatrixPos, notch = TRUE, outline = TRUE)
boxplot(MatrixNeg, notch = TRUE, outline = TRUE)

```

gives this result: enter image description here

From the knitr options: "error: (TRUE; logical) whether to preserve errors (from stop()); by default, the evaluation will not stop even in case of errors!! if we want R to stop on errors, we need to set this option to FALSE"

Upvotes: 4

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