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[#1972] windows pytest stalling at test_mr_classifier.py

Date:
2019-12-20 06:59

Priority:
3

State:
Open

Submitted by:
Charles Ballard (ccb63)

Assigned to:
Nobody (None)

Summary:
windows pytest stalling at test_mr_classifier.py

Detailed description
Stalled test test_mr_classifier.py, have skipped for now but needs checking
Stalled test test_mr_classifier.py, have skipped for now but needs checking

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Date: 2019-12-30 14:33 Sender: Charles Ballard Believe this was missing phmmer.exe
Date: 2019-12-20 13:31 Sender: Oleg Kovalevskiy I can confirm that this problem can be reproduced on Windows 7 machine, it is test_mr_hit.py indeed (not test_mr_classifier.py). Stack trace shows that it stalls forever in BioPython (Bio/SearchIO/HmmerIO/hmmer3_text.py), in read_forward() method that shall return next line containing anything apart from whitespace. Seems like an issue with reading files (or checking for whitespaces?) in Windows.
Date: 2019-12-20 12:22 Sender: Oleg Kovalevskiy According to the logs (https://anvil.softeng-support.ac.uk/jenkins/job/CCP4/job/win10/398/consoleFull), it seems to be test_mr_hit.py that hangs pytest, not test_mr_classifier.py (which seems to finish okay). test_mr_hit.py calls BioPython (SearchIO) to do search for homologues - is BioPython working well on Windows?

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