Merge pull request #3421 from harshagr70/GH-2758-fix-tidyverse

Fix "No Visible Binding for Global Variable" Warnings in lpjguess

models/lpjguess/R/model2netcdf.LPJGUESS.R

@@ -20,7 +20,7 @@ model2netcdf.LPJGUESS <- function(outdir, sitelat, sitelon, start_date, end_date
     PEcAn.logger::logger.error("No output files found at ", outdir)
   }
 
-  lpjguess.output <- lapply(file.path(outdir, lpjguess.out.files), read.table, header = TRUE, sep = "")
+  lpjguess.output <- lapply(file.path(outdir, lpjguess.out.files), utils::read.table, header = TRUE, sep = "")
   # n.outputs <- length(lpjguess.output)
   m.to.s <- 2592000
 

models/lpjguess/R/readStateBinary.LPJGUESS.R

@@ -208,13 +208,13 @@ readStateBinary <- function(out.path, npft){
   nofpatch <- readBin(zz, integer(), 1, size = 4)  
 
   for(pat in 1:nofpatch){
-    Patchpft_list[[pat]] <- getClass_Patchpft()
-    Vegetation_list[[pat]] <- getClass_Vegetation()
-    Individual_list[[pat]] <- getClass_Individual(Vegetation_list[[pat]]$indv)
-    Soil_list[[pat]] <- getClass_Soil()
-    Sompool_list[[pat]] <- getClass_Sompool()
-    SompoolCent_list[[pat]] <- getClass_SompoolCent() 
-    Fluxes_list[[pat]] <- getClass_Fluxes()
+    Patchpft_list[[pat]] <- getClass_Patchpft(zz, npft)
+    Vegetation_list[[pat]] <- getClass_Vegetation(zz)
+    Individual_list[[pat]] <- getClass_Individual(Vegetation_list[[pat]]$indv, zz)
+    Soil_list[[pat]] <- getClass_Soil(zz)
+    Sompool_list[[pat]] <- getClass_Sompool(zz)
+    SompoolCent_list[[pat]] <- getClass_SompoolCent(zz) 
+    Fluxes_list[[pat]] <- getClass_Fluxes(zz)
   }
 
   # close connection to the binary state file
@@ -226,7 +226,7 @@ readStateBinary <- function(out.path, npft){
 
 
 ##################### Class : Patchpft #####################
-getClass_Patchpft <- function(){
+getClass_Patchpft <- function(zz, npft){
 
   Patchpft <- list()
 
@@ -370,7 +370,7 @@ getClass_Patchpft <- function(){
 }
 
 ##################### Class : Vegetation #####################
-getClass_Vegetation <- function(){
+getClass_Vegetation <- function(zz){
 
   Vegetation <- list()
   Vegetation$indv <- readBin(zz, integer(), 1, size = 4)
@@ -380,7 +380,7 @@ getClass_Vegetation <- function(){
 
 
 ##################### Class : Individual #####################
-getClass_Individual <- function(nind){      #  nind <- Vegetation$indv 
+getClass_Individual <- function(nind, zz){      #  nind <- Vegetation$indv 
 
   Individual <- list()
 
@@ -670,7 +670,7 @@ getClass_Individual <- function(nind){      #  nind <- Vegetation$indv
 }
 
 ##################### Class : Soil #####################
-getClass_Soil <- function(){
+getClass_Soil <- function(zz){
   Soil <- list()
 
   # water content of soil layers [0=upper layer] as fraction of available water holding capacity;
@@ -748,7 +748,7 @@ getClass_Soil <- function(){
 
 
 ##################### Class : Sompool #####################
-getClass_Sompool <- function(){
+getClass_Sompool <- function(zz){
   Sompool <- list()
   npools <- 12
 
@@ -807,7 +807,7 @@ getClass_Sompool <- function(){
 
 
 ##################### Class : Sompool, CENTURY #####################
-getClass_SompoolCent <- function(){
+getClass_SompoolCent <- function(zz){
   SompoolCent <- list()
 
   # daily percolation (mm)
@@ -869,7 +869,7 @@ getClass_SompoolCent <- function(){
 
 
 ##################### Class : Fluxes #####################
-getClass_Fluxes <- function(){
+getClass_Fluxes <- function(zz){
   Fluxes <- list()
   #f.bytes <- bytes[1570:1667,]
   Fluxes$f1 <- readBin(zz, double(), 1, size = 8)

models/lpjguess/R/write.config.LPJGUESS.R

@@ -98,8 +98,8 @@ write.insfile.LPJGUESS <- function(settings, trait.values, rundir, outdir, run.i
   guessins  <- gsub("@GRID_FILE@", grid.file, guessins)
 
   pft_names <- sapply(settings$pfts, `[[`,"name")
-  load(system.file("lpjguess_params.Rdata",package = "PEcAn.LPJGUESS"))
-
+  lpjguess_param_data <- PEcAn.utils::load_local(system.file("lpjguess_params.Rdata",package = "PEcAn.LPJGUESS"))
+  lpjguess_param_list <- lpjguess_param_data$lpjguess_param_list
   # name and unit conversion
   trait.values <- pecan2lpjguess(trait.values)
 
@@ -183,7 +183,9 @@ write.insfile.LPJGUESS <- function(settings, trait.values, rundir, outdir, run.i
   if (end.year < 1850) {
     CO2 <- data.frame(start.year:end.year, rep(280, n.year))
   } else if (end.year < 2021) {
-    data(co2.1850.2020, package = "PEcAn.LPJGUESS")
+    co2_data <- new.env()
+    utils::data(co2.1850.2020, package = "PEcAn.LPJGUESS", envir = co2_data)
+    co2.1850.2020 <- co2_data$co2.1850.2020
     if (start.year < 1850) {
       CO2_preind <- data.frame(year = start.year:1849, ppm = rep(280, length(start.year:1849)))
       CO2_postind <- co2.1850.2020[1:which(co2.1850.2020[, 1] == end.year), ]
@@ -194,7 +196,7 @@ write.insfile.LPJGUESS <- function(settings, trait.values, rundir, outdir, run.i
   } else {
     PEcAn.logger::logger.severe("End year should be < 2021 for CO2")
   }
-  write.table(CO2, file = co2.file, row.names = FALSE, col.names = FALSE, sep = "\t", eol = "\n")
+  utils::write.table(CO2, file = co2.file, row.names = FALSE, col.names = FALSE, sep = "\t", eol = "\n")
   guessins <- gsub("@CO2_FILE@", co2.file, guessins)
 
   # write soil file path

models/lpjguess/tests/Rcheck_reference.log

@@ -45,35 +45,7 @@ Strong dependencies 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
-getClass_Fluxes: no visible binding for global variable ‘zz’
-getClass_Individual: no visible binding for global variable ‘zz’
-getClass_Patchpft: no visible binding for global variable ‘npft’
-getClass_Patchpft: no visible binding for global variable ‘zz’
-getClass_Soil: no visible binding for global variable ‘zz’
-getClass_Sompool: no visible binding for global variable ‘zz’
-getClass_SompoolCent: no visible binding for global variable ‘zz’
-getClass_Vegetation: no visible binding for global variable ‘zz’
-model2netcdf.LPJGUESS: no visible binding for global variable
-  ‘read.table’
-write.insfile.LPJGUESS: no visible binding for global variable
-  ‘lpjguess_param_list’
-write.insfile.LPJGUESS: no visible global function definition for
-  ‘data’
-write.insfile.LPJGUESS: no visible binding for global variable
-  ‘co2.1850.2020’
-write.insfile.LPJGUESS: no visible global function definition for
-  ‘write.table’
-Undefined global functions or variables:
-  co2.1850.2020 data lpjguess_param_list npft read.table write.table zz
-Consider adding
-  importFrom("utils", "data", "read.table", "write.table")
-to your NAMESPACE file.
-
-Found the following calls to data() loading into the global environment:
-File ‘PEcAn.LPJGUESS/R/write.config.LPJGUESS.R’:
-  data(co2.1850.2020, package = "PEcAn.LPJGUESS")
-See section ‘Good practice’ in ‘?data’.
+* checking R code for possible problems ... OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK