using data.tree to analyse Rprof files

profile.R

tmp <- tempfile(fileext = ".log")

x <- runif(10e5)
f <- function(x) c(mean(x), median(x), sd(x))
f2 <- function(x) {
  c(sum(x) / length(x),
    median.default(x),
    sqrt(sum((x - sum(x) / length(x))^2L) / (length(x) - 1L)))
}
Rprof(tmp, interval = 0.01)
for (i in 1:100) f(x)
for (i in 1:100) f2(x)
Rprof(NULL)
filename <- tmp

parse_log <- function(filename = "Rprof.out") {
  log <- scan(filename, what = "character", quote = "\"", sep = "\n",
              strip.white = TRUE, multi.line = FALSE, quiet = TRUE)
  if (length(log) == 1L)
    stop(sprintf("'%s' file is empty.", filename))
  interval <- as.numeric(strsplit(log[1L],split = "=", fixed = TRUE)[[1L]][2L]) / 1e06
  log <- log[-1L]
  log <- log[!grepl("^#", log)]
  calls <- unique(log)
  real.time <- tabulate(match(log, calls)) * interval
  total.time <- sum(real.time)
  pct.time <- real.time / total.time
  calls <- lapply(strsplit(calls, split = " ", fixed = TRUE), rev)
  calls <- vapply(calls, function(x) paste(c("calls", x), collapse = "/"), character(1L))
  structure(data.frame(pathString = calls, real = real.time, percent = pct.time, stringsAsFactors = FALSE),
            total.time = total.time)
}
#detach("package:data.tree")
#remove.packages("data.tree")
#devtools::install_github("gluc/data.tree", ref = "dev")

library(data.tree)
packageVersion("data.tree")
tree <- FromDataFrameTable(parse_log(tmp))
#make a copy of real, so we can verify the results later
tree$Set(realOrig = tree$Get("real"))
#on all but leaf nodes, sum up real from children, and add it to own time (if available)
tree$Do(function(node) node$real <- ifelse(is.null(node$real), 0, node$real) + Aggregate(node, "real", sum),
        traversal = "post-order", filterFun = isNotLeaf)
print(tree, "realOrig", "real")

result.txt

                                               levelName realOrig  real
1  calls                                                       NA 14.66
2   °--source                                                  NA 14.66
3       °--withVisible                                         NA 14.66
4           °--eval                                            NA 14.66
5               °--eval                                        NA 14.66
6                   ¦--f                                       NA  7.18
7                   ¦   ¦--median                            0.01  6.12
8                   ¦   ¦   °--median.default                  NA  6.11
9                   ¦   ¦       ¦--mean                        NA  5.05
10                  ¦   ¦       ¦   °--sort                    NA  5.05
11                  ¦   ¦       ¦       °--sort.default        NA  5.05
12                  ¦   ¦       ¦           °--sort.int      4.37  5.05
13                  ¦   ¦       ¦               ¦--is.na     0.20  0.40
14                  ¦   ¦       ¦               °--any       0.14  0.28
15                  ¦   ¦       ¦--is.na                     0.43  0.86
16                  ¦   ¦       °--any                       0.10  0.20
17                  ¦   ¦--sd                                  NA  0.62
18                  ¦   ¦   °--var                           0.60  0.62
19                  ¦   ¦       °--is.data.frame             0.01  0.02
20                  ¦   °--mean                                NA  0.44
21                  ¦       °--mean.default                  0.22  0.44
22                  °--f2                                      NA  7.48
23                      ¦--median.default                      NA  6.00
24                      ¦   ¦--mean                            NA  5.12
25                      ¦   ¦   °--sort                        NA  5.12
26                      ¦   ¦       °--sort.default            NA  5.12
27                      ¦   ¦           °--sort.int          4.34  5.12
28                      ¦   ¦               ¦--is.na         0.29  0.58
29                      ¦   ¦               °--any           0.10  0.20
30                      ¦   ¦--is.na                         0.32  0.64
31                      ¦   °--any                           0.12  0.24
32                      ¦---                                 0.10  0.20
33                      ¦--^                                 0.28  0.56
34                      °--sum                               0.36  0.72