Error on glide project

[Ivan-Veselov]

Error happened during processing of commit bumptech/glide@86ea385

ERROR [org.jetbrains.research.groups.ml_methods.refactoring.detection.tools.DefaultBranchesDetectionTool.detect] - Error occurred during refactoring detection for repository: https://github.com/bumptech/glide.git
java.lang.RuntimeException: org.eclipse.jgit.api.errors.CheckoutConflictException: Checkout conflict with files: 
third_party/disklrucache
	at org.refactoringminer.api.RefactoringHandler.handleException(RefactoringHandler.java:50)
	at org.refactoringminer.rm1.GitHistoryRefactoringMinerImpl.detect(GitHistoryRefactoringMinerImpl.java:102)
	at org.refactoringminer.rm1.GitHistoryRefactoringMinerImpl.detectAll(GitHistoryRefactoringMinerImpl.java:280)
	at org.jetbrains.research.groups.ml_methods.refactoring.detection.tools.RMiner.detect(RMiner.java:181)
	at org.jetbrains.research.groups.ml_methods.refactoring.detection.tools.RMiner.detect(RMiner.java:35)
	at org.jetbrains.research.groups.ml_methods.refactoring.detection.tools.DefaultBranchesDetectionTool.detect(DefaultBranchesDetectionTool.java:46)
	at org.jetbrains.research.groups.ml_methods.refactoring.detection.RefactoringDetectionApplication.run(RefactoringDetectionApplication.java:71)
	at org.jetbrains.research.groups.ml_methods.refactoring.detection.RefactoringDetectionApplication.main(RefactoringDetectionApplication.java:31)
Caused by: org.eclipse.jgit.api.errors.CheckoutConflictException: Checkout conflict with files: 
third_party/disklrucache
	at org.eclipse.jgit.api.CheckoutCommand.call(CheckoutCommand.java:276)
	at org.refactoringminer.util.GitServiceImpl.checkout(GitServiceImpl.java:120)
	at org.refactoringminer.rm1.GitHistoryRefactoringMinerImpl.detectRefactorings(GitHistoryRefactoringMinerImpl.java:134)
	at org.refactoringminer.rm1.GitHistoryRefactoringMinerImpl.detect(GitHistoryRefactoringMinerImpl.java:97)
	... 6 more
Caused by: org.eclipse.jgit.errors.CheckoutConflictException: Checkout conflict with files: 
third_party/disklrucache
	at org.eclipse.jgit.dircache.DirCacheCheckout.doCheckout(DirCacheCheckout.java:467)
	at org.eclipse.jgit.dircache.DirCacheCheckout.checkout(DirCacheCheckout.java:449)
	at org.eclipse.jgit.api.CheckoutCommand.call(CheckoutCommand.java:272)
	... 9 more

[Ivan-Veselov]

The problem is in git submodules.
Git.cloneRepository().setDirectory(new File("/tmp/glide")).setURI("https://github.com/bumptech/glide.git").setCloneAllBranches(true).call();
Such code with Eclipse git API clones repository with deleted submodules. This is exactly what happens inside RMiner. After that the problem arises only on mentioned commit.

[Ivan-Veselov]

Adding setCloneSubmodules(true) to command builder solves the problem.

[Ivan-Veselov]

But after that new problems arise.

[Ivan-Veselov]

error: The following untracked working tree files would be overwritten by checkout:
	third_party/disklrucache/LICENSE
	third_party/disklrucache/README.third_party
Please move or remove them before you switch branches.
Aborting

[Ivan-Veselov]

Problem is due to the fact that third_party/disklrucache/LICENSE and third_party/disklrucache/README.third_party were in repository until bumptech/glide@86ea385. This raises conflicts during checkout on parent of that commit.