fix check warnings/notes

DESCRIPTION

@@ -11,7 +11,9 @@ RoxygenNote: 5.0.1
 Imports:
     simmer (>= 3.2.0),
     magrittr,
-    dplyr
+    dplyr,
+    methods,
+    utils
 Suggests:
     knitr,
     rmarkdown,

R/core.R

@@ -22,7 +22,7 @@ simmer_optim <- function(model,
   if (length(params) == 0)
     stop("Please supply parameters to optimize over.")
 
-  control <- modifyList(optim_control(), control)
+  control <- utils::modifyList(optim_control(), control)
 
   r<-method(model = model,
             direction = direction,
@@ -32,7 +32,7 @@ simmer_optim <- function(model,
             control = control,
             ...)
 
-  if(!is(r, "MethodResults"))
+  if(!methods::is(r, "MethodResults"))
     stop("Optimization method should return a MethodResults object (created by 'method_results')")
 
   r
@@ -55,9 +55,9 @@ run_instance <- function(model, control, params){
 
   if(control$parallel){
     envs <- parallel::mclapply(1:rep, function(i){
-      env <- do.call(simmer::run, c(
-        list(env = eval(body(model), envir = temp_env)),
-        run_args))
+      env <- do.call(simmer::run,
+                     c(list(.env = eval(body(model), envir = temp_env)),
+                       run_args))
       simmer::wrap(env)
     }, mc.set.seed = F)
   } else {
@@ -78,7 +78,7 @@ run_instance <- function(model, control, params){
 #'
 #' @export
 objective_evaluator<-function(envs, objective){
-  if(is(objective, "funcArgs")){
+  if(methods::is(objective, "funcArgs")){
     do.call(objective$f, c(list(envs=envs), objective$args))
   } else {
     do.call(objective, list(envs=envs))
@@ -96,7 +96,7 @@ constraints_evaluator<-function(envs, constraints){
     stop("Please supply a list of constraint evaluation functions")
 
   lapply(1:length(constraints), function(i){
-    if(is(constraints[[i]], "funcArgs")){
+    if(methods::is(constraints[[i]], "funcArgs")){
       do.call(constraints[[i]]$f, c(list(envs = envs), constraints[[i]]$args))
     } else {
       do.call(constraints[[i]], list(envs=envs))

R/de_optim.R

@@ -36,7 +36,7 @@ de_optim <- function(model,
   lower_bounds <- sapply(params, function(x) x[1])
   upper_bounds <- sapply(params, function(x) x[length(x)])
   param_types <- sapply(params, function(x){
-    if(is(x, "ParDiscrete")){
+    if(methods::is(x, "ParDiscrete")){
       "ParDiscrete"
     } else {
       "ParContinuous"

R/grid_optim.R

@@ -16,7 +16,7 @@ grid_optim <- function(model, direction = c("min", "max"), objective, constraint
 
   if(control$verbose){
     cat("Running grid optimization procedure", "\n")
-    pb <- txtProgressBar(style=3)
+    pb <- utils::txtProgressBar(style=3)
   }
 
 
@@ -37,7 +37,7 @@ grid_optim <- function(model, direction = c("min", "max"), objective, constraint
         index = i
       )
 
-      if(control$verbose) setTxtProgressBar(pb, i/NROW(search_grid))
+      if(control$verbose) utils::setTxtProgressBar(pb, i/NROW(search_grid))
       res
     })
 

R/measures.R

@@ -7,7 +7,7 @@
 msr_arrivals_finished<-function(envs, agg = mean){
   tmp <- simmer::get_mon_arrivals(envs) %>%
     dplyr::group_by_("replication") %>%
-    dplyr::summarise(finished = n())
+    dplyr::summarise_(finished = "n()")
 
   tmp$finished %>%
     agg
@@ -52,11 +52,11 @@ msr_resource_utilization<-function(envs, name, agg=mean){
     simmer::get_mon_resources(envs) %>%
     dplyr::group_by_("resource", "replication") %>%
     dplyr::arrange_("resource", "time", "replication") %>%
-    dplyr::mutate_("server_prev"  = lag("server", default = 0),
-            "next_time" = dplyr::lead("time"),
-            "step_time" = "next_time" - "time",
-            "usage_time_weighted" = "step_time" * "server",
-            "non_usage_time_weighted" = ifelse("server" == 0, "step_time", 0)) %>%
+    dplyr::mutate_("server_prev"  = "lag(server, default = 0)",
+                   "next_time" = "lead(time)",
+                   "step_time" = "next_time - time",
+                   "usage_time_weighted" = "step_time" * "server",
+                   "non_usage_time_weighted" = ifelse("server" == 0, "step_time", 0)) %>%
     dplyr::summarise_(utilization = sum("usage_time_weighted", na.rm=T) / sum("non_usage_time_weighted", "usage_time_weighted", na.rm=T)) %>%
     dplyr::group_by_("resource") %>%
     dplyr::summarise_(utilization = agg("utilization")) %>%

R/sa_optim.R

@@ -37,7 +37,7 @@ sa_optim <- function(model,
     upper_bounds <- sapply(params, function(x) x[length(x)])
 
     param_types <- sapply(params, function(x){
-      if(is(x, "ParDiscrete")){
+      if(methods::is(x, "ParDiscrete")){
         "ParDiscrete"
       } else {
         "ParContinuous"