diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 8848edcc89..1261cd1df4 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -1727,7 +1727,7 @@ def convert_name(name, upper=False):
 
 
 def adjust_permissions(provided_path, permission_bits, add=True, onlyfiles=False, onlydirs=False, recursive=True,
-                       group_id=None, relative=True, ignore_errors=False, skip_symlinks=None):
+                       group_id=None, relative=True, ignore_errors=False):
     """
     Change permissions for specified path, using specified permission bits
 
@@ -1744,11 +1744,6 @@ def adjust_permissions(provided_path, permission_bits, add=True, onlyfiles=False
     and directories (if onlyfiles is False) in path
     """
 
-    if skip_symlinks is not None:
-        depr_msg = "Use of 'skip_symlinks' argument for 'adjust_permissions' is deprecated "
-        depr_msg += "(symlinks are never followed anymore)"
-        _log.deprecated(depr_msg, '4.0')
-
     provided_path = os.path.abspath(provided_path)
 
     if recursive:
@@ -2078,13 +2073,6 @@ def path_matches(path, paths):
     return False
 
 
-def rmtree2(path, n=3):
-    """Wrapper around shutil.rmtree to make it more robust when used on NFS mounted file systems."""
-
-    _log.deprecated("Use 'remove_dir' rather than 'rmtree2'", '5.0')
-    remove_dir(path)
-
-
 def find_backup_name_candidate(src_file):
     """Returns a non-existing file to be used as destination for backup files"""
 
@@ -2191,11 +2179,6 @@ def cleanup(logfile, tempdir, testing, silent=False):
         print_msg(msg, log=None, silent=testing or silent)
 
 
-def copytree(src, dst, symlinks=False, ignore=None):
-    """DEPRECATED and removed. Use copy_dir"""
-    _log.deprecated("Use 'copy_dir' rather than 'copytree'", '4.0')
-
-
 def encode_string(name):
     """
     This encoding function handles funky software names ad infinitum, like: