Appending error messages to log file while running multiple script components in R

Question

I am attempting to write error messages for my script to a log file. It works when I do:

test <- file("error_file.log", open = "wt")

sink(test, type = "message")

try(data <- read.delim("genes2.txt",

                   header = TRUE,

                   as.is = TRUE))

sink(type = "message", append = TRUE)

close(test)

However, when I add an additional component to the script, it does not append both error messages. In this case both input files do not exist and should give a "no such file directory" for each file. Here is my attempt for both input files:

enter code heretest <- file("error_file.log", open = "wt")



sink(test, type = "message")



try(data <- read.delim("genes2.txt",

                       header = TRUE,

                       as.is = TRUE))



sink(type = "message", append = TRUE)

close(test)



test2 <- file("error_file.log", open = "wt")

sink(test2, type = "message")



try(variables <- read.delim("Book3.txt",

                            header = TRUE, 

                            as.is = TRUE,

                            check.names = FALSE,

                            text = TRUE,

                            na.strings = c("", NA)))



sink(type = "message", append = TRUE)

close(test2)

Thank you!

P.s. would it be possible to customize my own error messages for each try()?

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Answer 1

Try using this, it'll append both the messages to error_file.log:-

test <- file("error_file.log", open = "wt")
sink(test, append = TRUE, type = "message")


try(data <- read.delim("genes2.txt",
                       header = TRUE,
                       as.is = TRUE))


try(variables <- read.delim("Book3.txt",
                            header = TRUE, 
                            as.is = TRUE,
                            check.names = FALSE,
                            text = TRUE,
                            na.strings = c("", NA)))


sink(type = "message")

So, error file would have:-

Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'genes2.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'Book3.txt': No such file or directory

I hope this solves your problem.

The trick is just open your log file and sink once in the begining. And, close sink in the end.

Appending error messages to log file while running multiple script components in R

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