diff --git a/komodo/lint.py b/komodo/lint.py
index 28719b5a..920d2830 100755
--- a/komodo/lint.py
+++ b/komodo/lint.py
@@ -93,9 +93,10 @@ def lint(
             maintainers.append(komodo_exception.error)
 
     if check_dependencies:
+        all_dependencies = dict(release_file.content.items())
         pypi_dependencies = {
             name: version
-            for name, version in release_file.content.items()
+            for name, version in all_dependencies.items()
             if repository_file.content.get(name, {}).get(version, {}).get("source")
             == "pypi"
         }
@@ -105,7 +106,7 @@ def lint(
             full_python_version = yaml.safe_load(f)[python_version]
 
         dependencies = PypiDependencies(
-            pypi_dependencies, python_version=full_python_version
+            pypi_dependencies, all_dependencies, python_version=full_python_version
         )
         for name, version in release_file.content.items():
             if (
diff --git a/komodo/pypi_dependencies.py b/komodo/pypi_dependencies.py
index 838ef250..9c90f1ed 100644
--- a/komodo/pypi_dependencies.py
+++ b/komodo/pypi_dependencies.py
@@ -40,6 +40,7 @@ def format_full_version(info) -> str:
 class PypiDependencies:
     def __init__(
         self,
+        pypi_dependencies: Dict[str, str],
         to_install: Dict[str, str],
         python_version: str,
         cachefile: str = "./pypi_dependencies.yml",
@@ -51,9 +52,11 @@ def __init__(
         self._failed_requirements: Dict[Requirement, str] = {}
         self._used_packages = set()
 
-        self._to_install = to_install
-
         self._install_names = {canonicalize_name(name): name for name in to_install}
+        self._pypi_dependencies = {
+            canonicalize_name(name): version
+            for name, version in pypi_dependencies.items()
+        }
         self._to_install = {
             canonicalize_name(name): version for name, version in to_install.items()
         }
@@ -70,7 +73,7 @@ def __init__(
         self._user_specified = {}
 
     def _update_package_sets(self, packages=None):
-        for package_name, version in packages or self._to_install.items():
+        for package_name, version in packages or self._pypi_dependencies.items():
             requirements = self._get_requirements(package_name, version)
             self._used_packages.add(package_name)
             for r in requirements: