Bug 2045231

Summary: bowtie: FTBFS in Fedora rawhide/f36: usr/include/c++/12/bits/stl_queue.h:725: std::priority_queue<>::const_reference std::priority_queue<>::top() const: Assertion '!this->empty()' failed
Product: [Fedora] Fedora Reporter: Fedora Release Engineering <releng>
Component: bowtieAssignee: Jun Aruga <jaruga>
Status: CLOSED WONTFIX QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: unspecified Docs Contact:
Priority: unspecified    
Version: rawhideCC: bloch, jaruga, ppisar
Target Milestone: ---   
Target Release: ---   
Hardware: Unspecified   
OS: Unspecified   
Whiteboard:
Fixed In Version: Doc Type: If docs needed, set a value
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Story Points: ---
Clone Of: Environment:
Last Closed: 2023-02-10 20:56:50 UTC Type: ---
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: --- Target Upstream Version:
Embargoed:
Bug Depends On:    
Bug Blocks: 1992484, 2045102, 2117176, 2168842    
Attachments:
Description Flags
build.log
none
root.log
none
state.log none

Description Fedora Release Engineering 2022-01-25 16:12:04 UTC 
bowtie failed to build from source in Fedora rawhide/f36

https://koji.fedoraproject.org/koji/taskinfo?taskID=81770042


For details on the mass rebuild see:

https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
Please fix bowtie at your earliest convenience and set the bug's status to
ASSIGNED when you start fixing it. If the bug remains in NEW state for 8 weeks,
bowtie will be orphaned. Before branching of Fedora 37,
bowtie will be retired, if it still fails to build.

For more details on the FTBFS policy, please visit:
https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/
Comment 1 Fedora Release Engineering 2022-01-25 16:12:08 UTC 
Created attachment 1853740 [details]
build.log

file build.log too big, will only attach last 32768 bytes
Comment 2 Fedora Release Engineering 2022-01-25 16:12:10 UTC 
Created attachment 1853741 [details]
root.log

file root.log too big, will only attach last 32768 bytes
Comment 3 Fedora Release Engineering 2022-01-25 16:12:12 UTC 
Created attachment 1853742 [details]
state.log
Comment 4 Ben Cotton 2022-02-08 20:45:23 UTC 
This bug appears to have been reported against 'rawhide' during the Fedora 36 development cycle.
Changing version to 36.
Comment 5 Petr Pisar 2022-09-19 10:50:02 UTC 
From a build.log:

./bowtie-build  --threads 2 --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie --debug   -s 1 -S --quiet -a .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
/usr/include/c++/12/bits/stl_queue.h:725: std::priority_queue<_Tp, _Sequence, _Compare>::const_reference std::priority_queue<_Tp, _Sequence, _Compare>::top() const [with _Tp = Branch*; _Sequence = std::vector<Branch*>; _Compare = CostCompare; const_reference = Branch* const&]: Assertion '!this->empty()' failed.
bowtie aborted with exitlevel 134
error: Bad exit status from /var/tmp/rpm-tmp.ScXcB6 (%check)
Comment 6 Jun Aruga 2022-09-19 11:51:21 UTC 
Thanks for the report!
Comment 7 Ben Cotton 2023-02-07 15:10:09 UTC 
This bug appears to have been reported against 'rawhide' during the Fedora Linux 38 development cycle.
Changing version to 38.
Comment 8 Jun Aruga 2023-02-09 14:53:36 UTC 
I confirmed this still happens on rawhide.
https://koji.fedoraproject.org/koji/taskinfo?taskID=97308929
Comment 9 Miro Hrončok 2023-02-10 20:56:50 UTC 
Automation has figured out the package is retired in rawhide.

If you like it to be unretired, please open a ticket at https://pagure.io/releng/new_issue?template=package_unretirement