diff --git a/coalib/bearlib/abstractions/Linter.py b/coalib/bearlib/abstractions/Linter.py
index 7cfc5fddbe..46703a8fc9 100644
--- a/coalib/bearlib/abstractions/Linter.py
+++ b/coalib/bearlib/abstractions/Linter.py
@@ -2,7 +2,7 @@
 from functools import partial, partialmethod
 import logging
 import inspect
-from itertools import chain, compress
+from itertools import chain
 import re
 import shutil
 from subprocess import check_call, CalledProcessError, DEVNULL
@@ -676,18 +676,45 @@ def run(self, filename=None, file=None, **kwargs):
                 self.debug("Running '{}'".format(
                     ' '.join(str(arg) for arg in arguments)))
 
-                output = run_shell_command(
+                result = run_shell_command(
                     arguments,
                     stdin=''.join(file) if options['use_stdin'] else None,
                     cwd=self.get_config_dir())
 
-                output = tuple(compress(
-                    output,
-                    (options['use_stdout'], options['use_stderr'])))
+                stdout, stderr = result
+
+                output = []
+
+                if options['use_stdout']:
+                    output.append(stdout)
+                elif stdout:
+                    logging.warning(
+                        '{}: Discarded stdout: {}'.format(
+                            self.__class__.__name__, stdout))
+                    stdout = ''
+
+                if options['use_stderr']:
+                    output.append(stderr)
+                elif stderr:
+                    logging.warning(
+                        '{}: Discarded stderr: {}'.format(
+                            self.__class__.__name__, stderr))
+                    stderr = ''
+
                 if options['strip_ansi']:
                     output = tuple(map(strip_ansi, output))
+                else:
+                    output = tuple(output)
+
                 if len(output) == 1:
                     output = output[0]
+
+                if not any([stdout, stderr]):
+                    logging.info(
+                        '{}: No output; skipping processing'.format(
+                            self.__class__.__name__))
+                    return
+
                 process_output_kwargs = FunctionMetadata.filter_parameters(
                     self._get_process_output_metadata(), kwargs)
                 return self.process_output(output, filename, file,
diff --git a/tests/bearlib/abstractions/LinterTest.py b/tests/bearlib/abstractions/LinterTest.py
index d6d87319c7..2b6b600052 100644
--- a/tests/bearlib/abstractions/LinterTest.py
+++ b/tests/bearlib/abstractions/LinterTest.py
@@ -298,7 +298,13 @@ def create_arguments(filename, file, config_file):
         uut = (linter(sys.executable, use_stdout=True)
                (TestLinter)
                (self.section, None))
-        uut.run('', [])
+
+        with self.assertLogs('', level='DEBUG') as cm:
+            uut.run('', [])
+
+        self.assertEqual(cm.output, [
+            'WARNING:root:TestLinter: Discarded stderr: hello stderr\n',
+            ])
 
         process_output_mock.assert_called_once_with('hello stdout\n', '', [])
         process_output_mock.reset_mock()
@@ -306,7 +312,13 @@ def create_arguments(filename, file, config_file):
         uut = (linter(sys.executable, use_stdout=False, use_stderr=True)
                (TestLinter)
                (self.section, None))
-        uut.run('', [])
+
+        with self.assertLogs('', level='DEBUG') as cm:
+            uut.run('', [])
+
+        self.assertEqual(cm.output, [
+            'WARNING:root:TestLinter: Discarded stdout: hello stdout\n',
+            ])
 
         process_output_mock.assert_called_once_with('hello stderr\n', '', [])
         process_output_mock.reset_mock()
@@ -320,6 +332,95 @@ def create_arguments(filename, file, config_file):
         process_output_mock.assert_called_once_with(('hello stdout\n',
                                                      'hello stderr\n'), '', [])
 
+    def test_no_output(self):
+        process_output_mock = Mock()
+        logging.getLogger().setLevel(logging.DEBUG)
+
+        class TestLinter:
+
+            @staticmethod
+            def process_output(output, filename, file):
+                process_output_mock(output, filename, file)
+
+            @staticmethod
+            def create_arguments(filename, file, config_file):
+                return '-c', ''
+
+        uut = (linter(sys.executable, use_stdout=True, use_stderr=True)
+               (TestLinter)
+               (self.section, None))
+
+        with self.assertLogs('', level='DEBUG') as cm:
+            uut.run('', [])
+
+            process_output_mock.assert_not_called()
+
+        self.assertEqual(cm.output, [
+            'INFO:root:TestLinter: No output; skipping processing',
+            ])
+
+    def test_discarded_stderr(self):
+        process_output_mock = Mock()
+        logging.getLogger().setLevel(logging.DEBUG)
+
+        class TestLinter:
+
+            @staticmethod
+            def process_output(output, filename, file):
+                process_output_mock(output, filename, file)
+
+            @staticmethod
+            def create_arguments(filename, file, config_file):
+                code = '\n'.join(['import sys',
+                                  "print('hello stderr', file=sys.stderr)",
+                                  ])
+                return '-c', code
+
+        uut = (linter(sys.executable, use_stdout=True, use_stderr=False)
+               (TestLinter)
+               (self.section, None))
+
+        with self.assertLogs('', level='DEBUG') as cm:
+            uut.run('', [])
+
+            process_output_mock.assert_not_called()
+
+        self.assertEqual(cm.output, [
+            'WARNING:root:TestLinter: Discarded stderr: hello stderr\n',
+            'INFO:root:TestLinter: No output; skipping processing',
+            ])
+
+    def test_discarded_stdout(self):
+        process_output_mock = Mock()
+        logging.getLogger().setLevel(logging.DEBUG)
+
+        class TestLinter:
+
+            @staticmethod
+            def process_output(output, filename, file):
+                process_output_mock(output, filename, file)
+
+            @staticmethod
+            def create_arguments(filename, file, config_file):
+                code = '\n'.join(['import sys',
+                                  "print('hello stdout', file=sys.stdout)",
+                                  ])
+                return '-c', code
+
+        uut = (linter(sys.executable, use_stdout=False, use_stderr=True)
+               (TestLinter)
+               (self.section, None))
+
+        with self.assertLogs('', level='DEBUG') as cm:
+            uut.run('', [])
+
+            process_output_mock.assert_not_called()
+
+        self.assertEqual(cm.output, [
+            'WARNING:root:TestLinter: Discarded stdout: hello stdout\n',
+            'INFO:root:TestLinter: No output; skipping processing',
+            ])
+
     def test_strip_ansi(self):
         process_output_mock = Mock()