Errors in running code in vignettes:
when running code in 'SimInf.Rnw'

> options(prompt = "R> ", continue = "+  ", width = 70, 
+     useFancyQuotes = FALSE)

> library("SimInf")

> n <- 1000

> u0 <- data.frame(S = rep(999, n), I = rep(1, n), R = rep(0, 
+     n))

> tspan <- seq(from = 1, to = 180, by = 7)

> model <- SIR(u0 = u0, tspan = tspan, beta = 0.16, 
+     gamma = 0.077)

> set.seed(123)

> set_num_threads(1)

> result <- run(model = model)

> result
Model: SIR
Number of nodes: 1000
Number of transitions: 2
Number of scheduled events: 0

Local data
----------
 Parameter Value
 beta      0.160
 gamma     0.077

Compartments
------------
    Min. 1st Qu. Median  Mean 3rd Qu.  Max.
 S 108.0   368.0  993.0 755.4   999.0 999.0
 I   0.0     0.0    1.0  30.4    38.0 235.0
 R   0.0     1.0    5.0 214.2   484.0 891.0

> pdf("SimInf-SIR-I.pdf", width = 10, height = 5)

> plot(result)

> dev.off()
null device 
          1 

> pdf("SimInf-SIR-II.pdf", width = 10, height = 5)

> plot(result, index = 1:10, range = FALSE)

> dev.off()
null device 
          1 

> head(trajectory(model = result, index = 1))
  node time   S  I  R
1    1    1 999  1  0
2    1    8 998  1  1
3    1   15 991  8  1
4    1   22 973 21  6
5    1   29 935 42 23
6    1   36 886 61 53

> events <- data.frame(event = c("enter", "extTrans", 
+     "exit", "enter"), time = c(2, 3, 4, 4), node = c(3, 1, 2, 
+     1), dest = c(0, 3, 0, 0) .... [TRUNCATED] 

> events
     event time node dest n proportion select shift
1    enter    2    3    0 5        0.0      1     0
2 extTrans    3    1    3 7        0.0      4     0
3     exit    4    2    0 0        0.2      4     0
4    enter    4    1    0 1        0.0      2     0

> u0 <- data.frame(S = rep(0, 5), I = rep(0, 5), R = rep(0, 
+     5))

> add <- data.frame(event = "enter", time = rep(1:10, 
+     each = 5), node = 1:5, dest = 0, n = 1:5, proportion = 0, 
+     select = 1, shift = 0)

> infect <- data.frame(event = "enter", time = 25, node = 5, 
+     dest = 0, n = 1, proportion = 0, select = 2, shift = 0)

> move <- data.frame(event = "extTrans", time = 35:45, 
+     node = c(5, 5, 5, 5, 4, 4, 4, 3, 3, 2, 1), dest = c(4, 3, 
+         3, 1, 3, 2, 1, 2, 1 .... [TRUNCATED] 

> remove <- data.frame(event = "exit", time = c(70, 
+     110), node = rep(1:5, each = 2), dest = 0, n = 0, proportion = 0.2, 
+     select = 4, shif .... [TRUNCATED] 

> events = rbind(add, infect, move, remove)

> model <- SIR(u0 = u0, tspan = 1:180, events = events, 
+     beta = 0.16, gamma = 0.077)

> set.seed(3)

> set_num_threads(1)

> result <- run(model)

> pdf("SimInf-SIR-events-I.pdf", width = 10, height = 5)

> plot(result, index = 1:5, range = FALSE)

> dev.off()
null device 
          1 

> model_no_infected <- SIR(u0 = u0, tspan = 1:180, events = rbind(add, 
+     move, remove), beta = 0.16, gamma = 0.077)

> set.seed(3)

> set_num_threads(1)

> result_no_infected <- run(model_no_infected)

> pdf("SimInf-SIR-events-II.pdf", width = 10, height = 5)

> plot(result_no_infected, index = 1:5, range = FALSE)

> dev.off()
null device 
          1 

> set.seed(123)

> set_num_threads(1)

> mean(replicate(n = 1000, {
+     nI <- trajectory(run(model = model), index = 1:4)$I
+     sum(nI) > 0
+ }))
[1] 0.477

> data("nodes", package = "SimInf")

> u0 <- u0_SISe()

> events <- events_SISe()

> d_ik <- distance_matrix(x = nodes$x, y = nodes$y, 
+     cutoff = 2500)

> set.seed(123)

> i <- sample(x = 1:1600, size = 160)

> u0$I[i] <- as.integer(u0$S[i] * 0.05)

> u0$S[i] <- u0$S[i] - u0$I[i]

> model <- SISe_sp(u0 = u0, tspan = 1:1460, events = events, 
+     phi = 0, upsilon = 0.012, gamma = 0.1, alpha = 1, beta_t1 = 0.1, 
+     beta_t2 =  .... [TRUNCATED] 

> transitions <- c("S -> b*S*I/(S+I+R) -> I", "I -> g*I -> R")

> compartments <- c("S", "I", "R")

> n <- 1000

> u0 <- data.frame(S = rep(99, n), I = rep(5, n), R = rep(0, 
+     n))

> model <- mparse(transitions = transitions, compartments = compartments, 
+     gdata = c(b = 0.16, g = 0.077), u0 = u0, tspan = 1:180)

> set.seed(123)

> set_num_threads(1)

> result <- run(model = model)
Warning in system2(file.path(R.home("bin"), "Rcmd.exe"), args, ...) :
  running command '"C:/msys64/home/tomas/ucrt3/svn/ucrt3/R_PACK~1/rinst/bin/x64/Rcmd.exe" SHLIB --output="C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/SimInf/tmp/RtmpEvfTv1/SimInf_288d0610151a3.dll" "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/SimInf/tmp/RtmpEvfTv1/SimInf_288d0610151a3.c"' had status 1

  When sourcing 'SimInf.R':
Error: Warning message:In system(cmd) : 'make' not found
Execution halted

  'SimInf.Rnw' using 'UTF-8'... failed
  'scheduled-events.Rmd' using 'UTF-8'... OK