Fix : Linkages for no visible bindings warnings

models/linkages/R/model2netcdf.LINKAGES.R

@@ -15,9 +15,11 @@
 model2netcdf.LINKAGES <- function(outdir, sitelat, sitelon, start_date = NULL,
                                   end_date = NULL, pft_names = NULL) {
   # , PFTs) { logger.severe('NOT IMPLEMENTED')
-
+
+  ## Create a new enviroment 
+  linkages_env <- new.env()
   ### Read in model output in linkages format
-  load(file.path(outdir, "linkages.out.Rdata"))
+  load(file.path(outdir, "linkages.out.Rdata"),envir = linkages_env)
   # linkages.output.dims <- dim(linkages.output)
 
   ### Determine number of years and output timestep
@@ -47,21 +49,21 @@ model2netcdf.LINKAGES <- function(outdir, sitelat, sitelon, start_date = NULL,
     ## Setup outputs for netCDF file in appropriate units
     output <- list()
     ## standard variables: Carbon Pools
-    output[[1]]  <- ag.biomass[y, ]  # Above Ground Biomass in kgC/m2
-    output[[2]]  <- ag.biomass[y, ]  # Total Live Biomass in kgC/m2 (no distinction from AGB in linkages)
-    output[[3]]  <- total.soil.carbon[y, ]  # TotSoilCarb in kgC/m2
-    output[[4]]  <- c(ag.biomass[y, ], total.soil.carbon[y, ], leaf.litter[y, ], area[y, ])  # Carb Pools in kgC/m2
+    output[[1]]  <- linkages_env$ag.biomass[y, ]  # Above Ground Biomass in kgC/m2
+    output[[2]]  <- linkages_env$ag.biomass[y, ]  # Total Live Biomass in kgC/m2 (no distinction from AGB in linkages)
+    output[[3]]  <- linkages_env$total.soil.carbon[y, ]  # TotSoilCarb in kgC/m2
+    output[[4]]  <- c(linkages_env$ag.biomass[y, ], linkages_env$total.soil.carbon[y, ], linkages_env$leaf.litter[y, ], linkages_env$area[y, ])  # Carb Pools in kgC/m2
     output[[5]]  <- c("AGB", "Soil Organic Matter", "Leaf Litter", "LAI")  # poolname
-    output[[6]]  <- ag.npp[y, ]  # GWBI = NPP in linkages
-    output[[7]]  <- hetero.resp[y, ]  # HeteroResp in kgC/m^2/s
-    output[[8]]  <- ag.npp[y, ]  # NPP = GWBI in linkages
-    output[[9]]  <- nee[y, ]  # NEE #possibly questionable
-    output[[10]] <- et[y, ]  # Evap in kg/m^2/s
-    output[[11]] <- agb.pft[, y, ]
-    output[[12]] <- f.comp[, y]
-    output[[13]] <- area[y, ]  #LAI
-    output[[14]] <- water[y, ]  #soil moisture
-    output[[15]] <- abvgroundwood.biomass[y,] #AbvGroundWood just wood no leaves
+    output[[6]]  <- linkages_env$ag.npp[y, ]  # GWBI = NPP in linkages
+    output[[7]]  <- linkages_env$hetero.resp[y, ]  # HeteroResp in kgC/m^2/s
+    output[[8]]  <- linkages_env$ag.npp[y, ]  # NPP = GWBI in linkages
+    output[[9]]  <- linkages_env$nee[y, ]  # NEE #possibly questionable
+    output[[10]] <- linkages_env$et[y, ]  # Evap in kg/m^2/s
+    output[[11]] <- linkages_env$agb.pft[, y, ]
+    output[[12]] <- linkages_env$f.comp[, y]
+    output[[13]] <- linkages_env$area[y, ]  #LAI
+    output[[14]] <- linkages_env$water[y, ]  #soil moisture
+    output[[15]] <- linkages_env$abvgroundwood.biomass[y,] #AbvGroundWood just wood no leaves
     output[[16]] <- seq_along(pft_names) 
 
     # ******************** Declare netCDF variables ********************#
@@ -75,7 +77,7 @@ model2netcdf.LINKAGES <- function(outdir, sitelat, sitelon, start_date = NULL,
     dim.cpools <- ncdf4::ncdim_def("cpools", "", vals = 1:4, longname = "Carbon Pools")
     dim.cpools1 <- ncdf4::ncdim_def("cpools", "", vals = 1:4, longname = "Carbon Pools", create_dimvar = FALSE)
     #dim.pfts <- ncdim_def("pfts", "", vals = 1:nrow(agb.pft), longname = "PFTs", create_dimvar = FALSE)
-    dim.pfts <- ncdf4::ncdim_def(name = "pft", units = "unitless", vals = 1:length(agb.pft[, 1, 1]), longname = "Plant Functional Type", unlim = TRUE)
+    dim.pfts <- ncdf4::ncdim_def(name = "pft", units = "unitless", vals = 1:length(linkages_env$agb.pft[, 1, 1]), longname = "Plant Functional Type", unlim = TRUE)
 
 
     for (i in seq_along(output)) {

models/linkages/R/write_restart.LINKAGES.R

@@ -134,16 +134,21 @@ write_restart.LINKAGES <- function(outdir, runid, start.time, stop.time,
   }
   print(paste0("runid = ", runid))
 
+  # Create a new enviroment
+  linkages_env <- new.env()
   # load output
-  load(outfile)
+  load(outfile, envir = linkages_env)
 
-  ntrees <- ntrees.kill[, ncol(ntrees.kill), 1]  # number of trees
+  ntrees <- linkages_env$ntrees.kill[, ncol(linkages_env$ntrees.kill), 1]  # number of trees
 
   if(sum(ntrees)==0) {
     #reloads spin up if theres nothing in the output file
     print('No survivors. Reusing spinup.')
-    load(file.path(outdir, runid,list.files(file.path(outdir, runid))[grep(list.files(file.path(outdir, runid)),pattern='linkages')][1]))
-    ntrees <- ntrees.kill[, ncol(ntrees.kill), 1]  # number of trees
+    # new enviroment for spin up data 
+    linkages_env_spinup <- new.env()
+    spinup_file <- file.path(outdir, runid,list.files(file.path(outdir, runid))[grep(list.files(file.path(outdir, runid)),pattern='linkages')][1])
+    load(spinup_file, envir = linkages_env_spinup)
+    ntrees <- linkages_env_spinup$ntrees.kill[, ncol(linkages_env_spinup$ntrees.kill), 1]  # number of trees
 
   }
 
@@ -152,11 +157,11 @@ write_restart.LINKAGES <- function(outdir, runid, start.time, stop.time,
   tyl    <- tyl
   C.mat  <- C.mat
 
-  nogro  <- as.vector(nogro.save[, ncol(nogro.save), 1])  ## no growth indicator
+  nogro  <- as.vector(linkages_env$nogro.save[, ncol(linkages_env$nogro.save), 1])  ## no growth indicator
   ksprt  <- matrix(0, 1, nspec)  ## kill sprout indicator ## LOOK INTO THIS
-  iage   <- as.vector(iage.save[, ncol(iage.save), 1])  # individual age
+  iage   <- as.vector(linkages_env$iage.save[, ncol(linkages_env$iage.save), 1])  # individual age
 
-  dbh    <- as.vector(dbh.save[, ncol(dbh.save), 1])
+  dbh    <- as.vector(linkages_env$dbh.save[, ncol(linkages_env$dbh.save), 1])
 
   n.index <- c(rep(1, ntrees[1]))
   for (i in 2:length(settings$pfts)) {

models/linkages/tests/Rcheck_reference.log

@@ -50,37 +50,7 @@ Suggests or Enhances not in mainstream repositories:
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... NOTE
-model2netcdf.LINKAGES: no visible binding for global variable
-  ‘ag.biomass’
-model2netcdf.LINKAGES: no visible binding for global variable
-  ‘total.soil.carbon’
-model2netcdf.LINKAGES: no visible binding for global variable
-  ‘leaf.litter’
-model2netcdf.LINKAGES: no visible binding for global variable ‘area’
-model2netcdf.LINKAGES: no visible binding for global variable ‘ag.npp’
-model2netcdf.LINKAGES: no visible binding for global variable
-  ‘hetero.resp’
-model2netcdf.LINKAGES: no visible binding for global variable ‘nee’
-model2netcdf.LINKAGES: no visible binding for global variable ‘et’
-model2netcdf.LINKAGES: no visible binding for global variable ‘agb.pft’
-model2netcdf.LINKAGES: no visible binding for global variable ‘f.comp’
-model2netcdf.LINKAGES: no visible binding for global variable ‘water’
-model2netcdf.LINKAGES: no visible binding for global variable
-  ‘abvgroundwood.biomass’
-write_restart.LINKAGES: no visible binding for global variable
-  ‘ntrees.kill’
-write_restart.LINKAGES: no visible binding for global variable
-  ‘nogro.save’
-write_restart.LINKAGES: no visible binding for global variable
-  ‘iage.save’
-write_restart.LINKAGES: no visible binding for global variable
-  ‘dbh.save’
-Undefined global functions or variables:
-  abvgroundwood.biomass ag.biomass ag.npp agb.pft area
-  db.close db.open db.query dbh.save et f.comp
-  hetero.resp iage.save leaf.litter nee nogro.save
-  ntrees.kill total.soil.carbon water
+* checking R code for possible problems ... OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK