Added El Capitan Mac binary identifier to selection statement

R/remerge_binaries.R

@@ -0,0 +1,30 @@
+#' @title Remerge the binaries with the library files for macGLM
+#' 
+#' @description This function remerges the macGLM binary file with
+#' the libraries present in inst/extbin/macGLM/bin
+#' 
+#' @author Arianna Krinos
+#' @importFrom utils packageName
+remerge_binaries <- function() {
+  lib_path = system.file('extbin/macGLM/bin/', package=packageName())
+  glm_path = system.file("exec/macGLM", package = packageName())
+  files = list.files(lib_path)
+  try ( system(paste0("install_name_tool -add_rpath ",lib_path, " ", 
+                      glm_path)), silent = TRUE) # First try separate because possible
+                                                 # rpath added without libraries linked
+  try (
+    {
+      for (g in 1:length(files)) {
+        system(paste0("install_name_tool -change ", "@executable_path/", 
+                      files[g]," ", lib_path, files[g], " ", glm_path)) 
+        system(paste0("install_name_tool -change ", "/opt/local/lib/hdf5-18/", 
+                      files[g]," ", lib_path, files[g], " ", glm_path))
+        for (h in 1:length(files)) {
+          system(paste0("install_name_tool -change ", "@executable_path/", 
+                      files[h]," ", lib_path, files[h], " ", lib_path,"/", files[g]))
+          system(paste0("install_name_tool -change ", "/opt/local/lib/hdf5-18/", 
+                      files[h]," ", lib_path, files[h], " ", lib_path,"/", files[g]))
+        }
+      }
+    } , silent = TRUE)
+}

R/run_glm.R

@@ -35,8 +35,7 @@ run_glm <- function(sim_folder = '.', verbose=TRUE, args=character()){
 
 		return(run_glmWin(sim_folder, verbose, args))
 
-	}else if(.Platform$pkgType == "mac.binary" || 
-					 	.Platform$pkgType == "mac.binary.mavericks"){
+	}else if(length(grep("mac", .Platform$pkgType, ignore.case = TRUE)) > 0){
     maj_v_number <- as.numeric(strsplit(
                       Sys.info()["release"][[1]],'.', fixed = TRUE)[[1]][1])
     if (maj_v_number < 13.0){
@@ -84,32 +83,43 @@ run_glmWin <- function(sim_folder, verbose = TRUE, args){
 
 run_glmOSx <- function(sim_folder, verbose = TRUE, args){
   lib_path <- system.file('extbin/macGLM/bin', package=packageName())
-
   glm_path <- system.file('exec/macglm', package=packageName())
 
   # ship glm and libs to sim_folder
-  Sys.setenv(DYLD_FALLBACK_LIBRARY_PATH=lib_path)
+  #remerge_binaries() # tries to remerge binaries; if they are
+                     # already merged, nothing occurs
 
   origin <- getwd()
   setwd(sim_folder)
-
-  tryCatch({
-    if (verbose){
-      out <- system2(glm_path, wait = TRUE, stdout = "", 
-                     stderr = "", args = args)
-
-    } else {
-      out <- system2(glm_path, wait = TRUE, stdout = NULL, 
-                     stderr = NULL, args=args)
+  count = 1
+
+  while (count <= 2) {
+    if (count == 2) {
+      try(remerge_binaries(), silent = TRUE)
     }
-
-    setwd(origin)
-	return(out)
-  }, error = function(err) {
-    print(paste("GLM_ERROR:  ",err))
-
-    setwd(origin)
-  })
+    tryCatch({
+      if (verbose){
+        out <- system2(glm_path, wait = TRUE, stdout = "", 
+                       stderr = "", args = args)
+
+      } else {
+        out <- system2(glm_path, wait = TRUE, stdout = NULL, 
+                       stderr = NULL, args=args)
+      }
+
+      setwd(origin)
+	    if (out == 0) {
+      		return(out)
+            }
+    }, error = function(err) {
+      if (count != 1) {
+      	print(paste("GLM_ERROR:  ",err))
+
+      	setwd(origin)
+      }
+    })
+    count = count + 1
+  }
 }
 
 run_glmNIX <- function(sim_folder, verbose=TRUE, args){