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

[harshagr70]

This PR focuses on addressing "no visible binding for global variable" warnings specifically within the lpjguess package of the Pecan codebase , these warnings were not specifically from the tidyverse calls . These issues were identified during rcmdcheck::rcmdcheck() runs, and while some changes have been implemented, further guidance is needed for unresolved errors. , fixes a part of the issue #2758

Summary of Changes:

Scoped Variables:
Passed the ZZ variable as an argument in the relevant functions to resolve scoping issues flagged by R CMD check.

Namespace Updates:
Added required imports to the NAMESPACE file as suggested by rcmdcheck.

Log File Updates:
Updated the .log file to reflect the removal of errors for the issues that were fixed in this PR.

The following warnings remain unresolved and require input from maintainers:

write.insfile.LPJGUESS:
No visible binding for global variable: lpjguess_param_list.
No visible binding for global variable: co2.1850.2020.
Undefined global functions or variables:
co2.1850.2020 and lpjguess_param_list

These warnings may need clarification on:
Whether lpjguess_param_list and co2.1850.2020 should be explicitly declared as global variables or passed as arguments.

[infotroph]

Thanks for working on this! Instead of an importFrom directive let's follow PEcAn house style by finding these calls where they appear in the code and adding the utils namespace qualifier, so that write.table(df, filename,...) becomes utils::write.table(df, filename, ...) and so on. (In concept we'd like to do the same for all instances of the ncdf4::nc* functions imported below, but that can be a separate project)

But FYI we do use importFrom for cases that don't work at all in :: form (e.g. rlang's .data pronoun) or that do work but become a hassle (e.g. infix functions like %>%), so feel free to propose an importFrom where it seems like the right move.

However in those cases be aware you'll need to use Roxygen directives (e.g. #' @importFrom utils write.table in the Roxygen comments for the function that uses write.table) rather than edit NAMESPACE directly -- as written Roxygen will overwrite this change the next time it runs.

[harshagr70]

Thank you for the feedback! I’ll update the code to use utils::write.table and similar namespace qualifiers as per the PEcAn house style. I appreciate the clarification on using importFrom with Roxygen directives when needed—I'll keep this in mind for future contributions. I’ll make the changes and push the updates shortly. Thanks again !!

[infotroph]

Suggested change

	getClass_Patchpft <- function(zz,npft){
	getClass_Patchpft <- function(zz, npft){

[infotroph]

Suggested change

	getClass_Individual <- function(nind,zz){ # nind <- Vegetation$indv
	getClass_Individual <- function(nind, zz){ # nind <- Vegetation$indv

[harshagr70]

@infotroph i have added the changes as suggested !! and also checked for any errors by R CMD check . This fixes warnings in the lpjguess package but there are two more warnings on which i need your guidance ,

Whether lpjguess_param_list and co2.1850.2020 should be explicitly declared as global variables or any other alternative fix for this !!