Integrated ncdf4 required code.

DESCRIPTION

@@ -3,7 +3,8 @@ Title: Tools to Easily Read/Write NetCDF Files into/from Multidimensional R Arra
 Version: 0.0.2
 Authors@R: c(
     person("BSC-CNS", role = c("aut", "cph")),
-    person("Nicolau", "Manubens", , "nicolau.manubens@bsc.es", role = c("aut", "cre")))
+    person("Nicolau", "Manubens", , "nicolau.manubens@bsc.es", role = c("aut", "cre")),
+    person("David", "Pierce", , "david.pierce@ucsd.edu", role = c("ctb")))
 Description: Set of wrappers for the 'ncdf4' package to simplify and extend its reading/writing capabilities into/from multidimensional R arrays.
 Depends:
     R (>= 2.14.1)
@@ -15,3 +16,4 @@ URL: https://earth.bsc.es/gitlab/es/easyNCDF/wikis/home
 BugReports: https://earth.bsc.es/gitlab/es/easyNCDF/issues
 LazyData: true
 SystemRequirements: netcdf development libraries
+NeedsCompilation: yes

NAMESPACE

+useDynLib(easyNCDF)
 exportPattern("^[^\\.]")
 import(ncdf4, abind)
 importFrom("stats", "setNames")

R/NcToArray.R

@@ -203,16 +203,16 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
                 (length(file_object[['var']][[var_name]][['dim']]) > 1)) {
               start <- c(1, start)
               count <- c(-1, count)
-              original_ncvar_get_inner <- ncdf4:::ncvar_get_inner
-              assignInNamespace('ncvar_get_inner', .ncvar_get_inner, 'ncdf4')
+              ##original_ncvar_get_inner <- ncdf4:::ncvar_get_inner
+              ##assignInNamespace('ncvar_get_inner', .ncvar_get_inner, 'ncdf4')
             }
-            var_result <- do.call('[', c(list(ncvar_get(file_object, var_name, start, count, collapse_degen = FALSE)),
+            var_result <- do.call('[', c(list(.ncvar_get(file_object, var_name, start, count, collapse_degen = FALSE)),
                                          lapply(indices_to_take, function(x) if (is_single_na(x)) TRUE else x - min(x) + 1), list(drop = FALSE)))
-            # Support for character strings
-            if ((file_object[['var']][[var_name]][['prec']] == 'char') && 
-                (length(file_object[['var']][[var_name]][['dim']]) > 1)) {
-              assignInNamespace('ncvar_get_inner', original_ncvar_get_inner, 'ncdf4')
-            }
+            ### Support for character strings
+            ##if ((file_object[['var']][[var_name]][['prec']] == 'char') && 
+            ##    (length(file_object[['var']][[var_name]][['dim']]) > 1)) {
+            ##  assignInNamespace('ncvar_get_inner', original_ncvar_get_inner, 'ncdf4')
+            ##}
             #metadata <- c(metadata, structure(list(file_object$var[[var_name]]), .Names = var_name))
             names(dim(var_result)) <- names(indices_to_take)
             # Drop extra dims

cleanup

+#! /bin/sh
+
+rm -f config.* R/load.R src/Makevars
+rm -rf autom4te.cache

src/Makevars.in

+##PKG_CPPFLAGS=-I/path/to/netcdf/header
+##PKG_LIBS=-L/path/to/netcdf/lib -lnetcdf
+
+PKG_LIBS=@NETCDF_LDFLAGS@
+PKG_CPPFLAGS=@NETCDF_CPPFLAGS@
+

src/Makevars.win

+PKG_LIBS = -lnetcdf4 -L$(LIB_HDF5)/lib${R_ARCH} -lhdf5_hl -lhdf5 -lz