Fix overwriting /bin

pkg/dockerfile/fast_generator.go

@@ -334,7 +334,7 @@ func (g *FastGenerator) installApt(lines []string, aptTarFile string) ([]string,
 	// Install apt packages
 
 	if aptTarFile != "" {
-		lines = append(lines, "RUN --mount=from="+dockercontext.AptBuildContextName+",target="+buildTmpDir+" tar --no-overwrite-dir -xf \""+filepath.Join(buildTmpDir, aptTarFile)+"\" -C /")
+		lines = append(lines, "RUN --mount=from="+dockercontext.AptBuildContextName+",target="+buildTmpDir+" tar --keep-directory-symlink -xf \""+filepath.Join(buildTmpDir, aptTarFile)+"\" -C /")
 	}
 	return lines, nil
 }

pkg/dockerfile/fast_generator_test.go

@@ -227,7 +227,7 @@ func TestAptInstall(t *testing.T) {
 	dockerfile, err := generator.GenerateDockerfileWithoutSeparateWeights()
 	require.NoError(t, err)
 	dockerfileLines := strings.Split(dockerfile, "\n")
-	require.Equal(t, "RUN --mount=from=apt,target=/buildtmp tar --no-overwrite-dir -xf \"/buildtmp/apt.9a881b9b9f23849475296a8cd768ea1965bc3152df7118e60c145975af6aa58a.tar.zst\" -C /", dockerfileLines[5])
+	require.Equal(t, "RUN --mount=from=apt,target=/buildtmp tar --keep-directory-symlink -xf \"/buildtmp/apt.9a881b9b9f23849475296a8cd768ea1965bc3152df7118e60c145975af6aa58a.tar.zst\" -C /", dockerfileLines[5])
 }
 
 func TestValidateConfigWithBuildRunItems(t *testing.T) {

test-integration/test_integration/fixtures/zsh-package/cog.yaml

@@ -0,0 +1,7 @@
+build:
+  python_version: "3.12"
+  fast: true
+  system_packages:
+    - "zsh"
+  python_requirements: requirements.txt
+predict: "predict.py:Predictor"

test-integration/test_integration/fixtures/zsh-package/predict.py

@@ -0,0 +1,8 @@
+from cog import BasePredictor
+
+import os
+
+
+class Predictor(BasePredictor):
+    def predict(self) -> str:
+        return "hello " + ",".join(os.listdir("/bin"))

test-integration/test_integration/fixtures/zsh-package/requirements.txt

@@ -0,0 +1 @@
+torch==2.5.0

test-integration/test_integration/test_predict.py

@@ -432,3 +432,26 @@ def test_predict_optional_project(tmpdir_factory):
     # stdout should be clean without any log messages so it can be piped to other commands
     assert result.returncode == 0
     assert result.stdout == "hello No One\n"
+
+
+def test_predict_zsh_package(docker_image):
+    project_dir = Path(__file__).parent / "fixtures/zsh-package"
+    build_process = subprocess.run(
+        ["cog", "build", "-t", docker_image],
+        cwd=project_dir,
+        capture_output=True,
+    )
+    assert build_process.returncode == 0
+
+    result = subprocess.run(
+        ["cog", "predict", "--debug", docker_image],
+        cwd=project_dir,
+        check=True,
+        capture_output=True,
+        text=True,
+        timeout=DEFAULT_TIMEOUT,
+    )
+    # stdout should be clean without any log messages so it can be piped to other commands
+    assert result.returncode == 0
+    assert ",sh," in result.stdout
+    assert ",zsh," in result.stdout