fix warnings/notes in data.remote package

PecanProject · Sep 18, 2023 · 0e84cc8 · 0e84cc8
1 parent ce327b9
commit 0e84cc8
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Showing 3 changed files with 13 additions and 13 deletions.
diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
@@ -24,9 +24,9 @@ download.NLCD <- function(outdir, year = 2011, con = NULL) {
     ## before downloading, check if the file already exists on this host
     if (!is.null(con)) {
         library(PEcAn.DB)
-        chk <- dbfile.check(type = "Input", id = input.id, con = con)
+        chk <- PEcAn.DB::dbfile.check(type = "Input", id = input.id, con = con)
         if (nrow(chk) > 0) {
-            machines <- db.query(paste("SELECT * from machines where id in (", 
+            machines <- PEcAn.DB::db.query(paste("SELECT * from machines where id in (", 
                                        paste(chk$machine_id, sep = ","), ")"), con)
             if (PEcAn.remote::fqdn() %in% machines$hostname) {
                 ## record already exists on this host
@@ -49,7 +49,7 @@ download.NLCD <- function(outdir, year = 2011, con = NULL) {
         prefix <- table(sapply(strsplit(dir(data_dir), ".", fixed = TRUE), function(x) { x[1] }))
         prefix <- names(which.max(prefix))
         site.id <- 1000000676
-        return(dbfile.insert(data_dir, in.prefix = prefix, type = "Input", input.id, con, 
+        return(PEcAn.DB::dbfile.insert(data_dir, in.prefix = prefix, type = "Input", input.id, con, 
             reuse = TRUE))
     }
     return(data_dir)
@@ -80,9 +80,9 @@ extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 201
         } else {
             print(paste("Year not yet supported: ", year))
         }
-        chk <- dbfile.check(type = "Input", id = input.id, con = con)
+        chk <- PEcAn.DB::dbfile.check(type = "Input", id = input.id, con = con)
         if (nrow(chk) > 0) {
-            machines <- db.query(paste("SELECT * from machines where id in (",
+            machines <- PEcAn.DB::db.query(paste("SELECT * from machines where id in (",
                                        paste(chk$machine_id, sep = ","), ")"), con)
             if (PEcAn.remote::fqdn() %in% machines$hostname) {
                 ## record already exists on this host
@@ -104,14 +104,14 @@ extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 201
         print(paste("File not found:", filename))
         return(NULL)
     }
-    nlcd <- raster(filename)
+    nlcd <- raster::raster(filename)
 
     # transform points
-    sites <- SpatialPoints(coords = coords, proj4string = CRS("+proj=longlat +datum=WGS84"))
-    sites <- spTransform(sites, crs(nlcd))
+    sites <- sp::SpatialPoints(coords = coords, proj4string = sp::CRS("+proj=longlat +datum=WGS84"))
+    sites <- sp::spTransform(sites, raster::crs(nlcd))
 
     # extract
-    sum.raw <- table(extract(nlcd, sites, buffer = buffer))
+    sum.raw <- table(raster::extract(nlcd, sites, buffer = buffer))
     summ <- prop.table(sum.raw)
     mydf <- data.frame(cover = names(summ), percent = as.vector(summ), count = as.vector(sum.raw))
 

diff --git a/modules/data.remote/R/call_MODIS.R b/modules/data.remote/R/call_MODIS.R
@@ -283,7 +283,7 @@ call_MODIS <- function(var, product,
         fname <- paste(site_info$site_id[i], "/", product, "_", band, "_", start_date, "-", end_date, "_unfiltered.csv", sep = "")
       }
       fname <- file.path(outdir, fname)
-      write.csv(site, fname, row.names = FALSE)
+      utils::write.csv(site, fname, row.names = FALSE)
     }
 
   }

diff --git a/modules/data.remote/R/download.thredds.R b/modules/data.remote/R/download.thredds.R
@@ -69,7 +69,7 @@ download.thredds.AGB <- function(outdir = NULL, site_ids, run_parallel = FALSE,
     # option to save output dataset to directory for user.
     if (!(is.null(outdir)))
     {
-      write.csv(output, file = paste0(outdir, "THREDDS_", sub("^([^.]*).*", "\\1",basename(files[1])), "_site_", site, ".csv"), row.names = FALSE)
+      utils::write.csv(output, file = paste0(outdir, "THREDDS_", sub("^([^.]*).*", "\\1",basename(files[1])), "_site_", site, ".csv"), row.names = FALSE)
     }
 
     return(output)
@@ -86,8 +86,8 @@ download.thredds.AGB <- function(outdir = NULL, site_ids, run_parallel = FALSE,
     PEcAn.logger::logger.info(paste0("Running in parallel with: ", ncores))
     cl = parallel::makeCluster(ncores)
     doParallel::registerDoParallel(cl)
-    data = foreach(i = seq_along(mylat), .combine = rbind) %dopar% get_data(i)
-    stopCluster(cl)
+    data = foreach::foreach(i = seq_along(mylat), .combine = rbind) %dopar% get_data(i)
+    parallel::stopCluster(cl)
 
   } else {
     # setup sequential run