R -- Console output redirect does not (reliably) work from function call

Question

I wrote the following code to redirect console output to text file. All three commands' (dim, str, summary) output appears in the text file when I interactively run the code. However, when I place the code in a function and interactively run through a function call, only the str command outuput appears. This may be a buffering problem. Any suggestions?

Operating System : OS X 10.9.5 (Mavericks); R 3.1.1 GUI 1.65 Mavericks build (6784)

This code works...

con <- file("FileInfoLog.txt")
sink(con, append=TRUE)
sink(con, append=TRUE, type="message")

writeLines("\n\n\n===============================================================\n")
writeLines("Dimensions are ")
dim(db)
writeLines("\n\n\n===============================================================\n")
writeLines("Structure is ")
str(db)
writeLines("\n\n\n===============================================================\n")
writeLines("Summary is ")
summary(db)

# Restore output to console
sink(type="message")
sink()

This code does not reliably work...only the str() output appears in the text file.

getFileInfo <- function(db) {

    con <- file("FileInfoLog.txt")
    sink(con, append=TRUE)
    sink(con, append=TRUE, type="message")

    writeLines("\n\n\n===============================================================\n")
    writeLines("Dimensions are ")
    dim(db)
    writeLines("\n\n\n===============================================================\n")
    writeLines("Structure is ")
    str(db)
    writeLines("\n\n\n===============================================================\n")
    writeLines("Summary is ")
    summary(db)

    # Restore output to console
    sink(type="message")
    sink() 

}

FileInfoLog.txt from code that works...

===============================================================

Dimensions are [1] 28947 17

===============================================================

Structure is 'data.frame': 28947 obs. of 17 variables: $ store : int 2 2 2 2 2 2 2 2 2 2 ... $ brand : Factor w/ 3 levels "dominicks","minute.maid",..: 3 3 3 3 3 3 3 3 3 3 ... $ week : int 40 46 47 48 50 51 52 53 54 57 ... $ logmove : num 9.02 8.72 8.25 8.99 9.09 ... [...]

===============================================================

Summary is store brand week logmove feat price AGE60
Min. : 2.00 dominicks :9649 Min. : 40.0 Min. : 4.159 Min. :0.0000 Min. :0.520 Min. :0.05805
1st Qu.: 53.00 minute.maid:9649 1st Qu.: 70.0 1st Qu.: 8.490 1st Qu.:0.0000 1st Qu.:1.790 1st Qu.:0.12210
Median : 86.00 tropicana :9649 Median :101.0 Median : 9.034 Median :0.0000 Median :2.170 Median :0.17065
Mean : 80.88 Mean :100.5 Mean : 9.168 Mean :0.2373 Mean :2.282 Mean :0.17313
3rd Qu.:111.00 3rd Qu.:130.0 3rd Qu.: 9.765 3rd Qu.:0.0000 3rd Qu.:2.730 3rd Qu.:0.21395
Max. :137.00 Max. :160.0 Max. :13.482 Max. :1.0000 Max. :3.870 Max. :0.30740
[...]

FileInfoLog.txt from code that does not reliably work...

===============================================================

Dimensions are

===============================================================

Structure is 'data.frame': 28947 obs. of 17 variables: $ store : int 2 2 2 2 2 2 2 2 2 2 ... $ brand : Factor w/ 3 levels "dominicks","minute.maid",..: 3 3 3 3 3 3 3 3 3 3 ... $ week : int 40 46 47 48 50 51 52 53 54 57 ... $ logmove : num 9.02 8.72 8.25 8.99 9.09 ... [...]

===============================================================

Summary is

I thought the console output was relevant for the question, so I included it. I significantly shortened it though. Thanks for your remark. — Rick Gregory

MrFlick MrFlick · Accepted Answer · 2015-01-11T22:50:34

When you run interactively, the print() command is called implicitly on each result. When in interactive mode, this is not the case. You must call print() explicitly. So you would need print(dim(db)).

The str() function is different because it creates it's output via cat() and doesn't actually return anything.

If you are using the source() function to run your script, you can set echo=TRUE to keep the auto-printing behavior.

Also, rather than bothering with setting up sink() and capture.out() commands yourself. You might consider looking at knitr to make it nice looking reports with R code.

R -- Console output redirect does not (reliably) work from function call

1 Answers