Sporadic permission error on Windows when running preranked analysis

[dmitriikamaevqia]

Preranked analysis on Windows sometimes causes this error. My guess is you are trying to cleanup tmp directory while logger is sill writing into it

`C:\Users\abc\AppData\Local\Temp\ipykernel_4536\399291494.py:1: DeprecationWarning: processes is deprecated; use threads
preranked_result = gp.prerank(rnk=significant_genes,
2022-12-12 15:06:11,853 Duplicated values found in preranked stats: 34.79% of genes
The order of those genes will be arbitrary, which may produce unexpected results.

---

PermissionError Traceback (most recent call last)
File ~\AppData\Local\Programs\Python\Python39\lib\shutil.py:627, in _rmtree_unsafe(path, onerror)
626 try:
--> 627 os.unlink(fullname)
628 except OSError:

PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\Users\abc\AppData\Local\Temp\tmpgamkfkhl\gseapy.prerank.log'

During handling of the above exception, another exception occurred:

PermissionError Traceback (most recent call last)
File ~\AppData\Local\Programs\Python\Python39\lib\tempfile.py:805, in TemporaryDirectory._rmtree..onerror(func, path, exc_info)
804 try:
--> 805 _os.unlink(path)
806 # PermissionError is raised on FreeBSD for directories

PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\Users\abc\AppData\Local\Temp\tmpgamkfkhl\gseapy.prerank.log'

During handling of the above exception, another exception occurred:

NotADirectoryError Traceback (most recent call last)
Input In [10], in <cell line: 1>()
----> 1 preranked_result = gp.prerank(rnk=significant_genes,
2 gene_sets=gene_sets.copy(),
3 min_size=10,
4 max_size=10000,
5 processes=4,
6 no_plot=True)
7 gsea_df = preranked_result.res2d
8 gsea_df['Term'] = gsea_df.index

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\gseapy_init_.py:356, in prerank(rnk, gene_sets, outdir, pheno_pos, pheno_neg, min_size, max_size, permutation_num, weighted_score_type, ascending, threads, figsize, format, graph_num, no_plot, seed, verbose, *arg, **kwarg)
336 threads = kwarg["processes"]
337 pre = Prerank(
338 rnk,
339 gene_sets,
(...)
354 verbose,
355 )
--> 356 pre.run()
357 return pre

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\gseapy\gsea.py:464, in Prerank.run(self)
462 self._logger.info("Congratulations. GSEApy runs successfully................\n")
463 if self._outdir is None:
--> 464 self._tmpdir.cleanup()
466 return

File ~\AppData\Local\Programs\Python\Python39\lib\tempfile.py:834, in TemporaryDirectory.cleanup(self)
832 def cleanup(self):
833 if self._finalizer.detach():
--> 834 self._rmtree(self.name)

File ~\AppData\Local\Programs\Python\Python39\lib\tempfile.py:816, in TemporaryDirectory._rmtree(cls, name)
813 else:
814 raise
--> 816 _shutil.rmtree(name, onerror=onerror)

File ~\AppData\Local\Programs\Python\Python39\lib\shutil.py:759, in rmtree(path, ignore_errors, onerror)
757 # can't continue even if onerror hook returns
758 return
--> 759 return _rmtree_unsafe(path, onerror)

File ~\AppData\Local\Programs\Python\Python39\lib\shutil.py:629, in _rmtree_unsafe(path, onerror)
627 os.unlink(fullname)
628 except OSError:
--> 629 onerror(os.unlink, fullname, sys.exc_info())
630 try:
631 os.rmdir(path)

File ~\AppData\Local\Programs\Python\Python39\lib\tempfile.py:808, in TemporaryDirectory._rmtree..onerror(func, path, exc_info)
806 # PermissionError is raised on FreeBSD for directories
807 except (IsADirectoryError, PermissionError):
--> 808 cls._rmtree(path)
809 except FileNotFoundError:
810 pass

File ~\AppData\Local\Programs\Python\Python39\lib\tempfile.py:816, in TemporaryDirectory._rmtree(cls, name)
813 else:
814 raise
--> 816 _shutil.rmtree(name, onerror=onerror)

File ~\AppData\Local\Programs\Python\Python39\lib\shutil.py:759, in rmtree(path, ignore_errors, onerror)
757 # can't continue even if onerror hook returns
758 return
--> 759 return _rmtree_unsafe(path, onerror)

File ~\AppData\Local\Programs\Python\Python39\lib\shutil.py:610, in _rmtree_unsafe(path, onerror)
608 entries = list(scandir_it)
609 except OSError:
--> 610 onerror(os.scandir, path, sys.exc_info())
611 entries = []
612 for entry in entries:

File ~\AppData\Local\Programs\Python\Python39\lib\shutil.py:607, in _rmtree_unsafe(path, onerror)
605 def _rmtree_unsafe(path, onerror):
606 try:
--> 607 with os.scandir(path) as scandir_it:
608 entries = list(scandir_it)
609 except OSError:

NotADirectoryError: [WinError 267] The directory name is invalid: 'C:\Users\abc\AppData\Local\Temp\tmpgamkfkhl\gseapy.prerank.log'`

[zqfang]

That's weird. I'll check it.

[zqfang]

Fixed in new release v1.0.3