Packages should not write in the user’s home filespace (including clipboards), nor anywhere else on the file system apart from the R session’s temporary directory (or during installation in the location pointed to by TMPDIR: and such usage should be cleaned up). Installing into the system’s R installation (e.g., scripts to its bin directory) is not allowed.
Limited exceptions may be allowed in interactive sessions if the package obtains confirmation from the user.
From CRAN repository policy:
Therefore, changes are needed in
setup_directory()ModvegeSite$write_output()run_parameter_scan()