Bug 1674691

Summary: bfast: FTBFS in Fedora rawhide/f30: bfast/RGIndex.c:784: undefined reference to `pthread_create'
Product: [Fedora] Fedora Reporter: Fedora Release Engineering <releng>
Component: bfastAssignee: Petr Pisar <ppisar>
Status: CLOSED ERRATA QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: unspecified Docs Contact:
Priority: unspecified    
Version: rawhideCC: bloch, ppisar
Target Milestone: ---   
Target Release: ---   
Hardware: Unspecified   
OS: Unspecified   
Whiteboard:
Fixed In Version: bfast-0.7.0a-21.fc31 bfast-0.7.0a-21.fc30 Doc Type: If docs needed, set a value
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2019-07-24 00:58:26 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: 1674516    
Attachments:
Description Flags
build.log
none
root.log
none
state.log none

Description Fedora Release Engineering 2019-02-11 16:52:58 UTC
bfast failed to build from source in Fedora rawhide/f30

https://koji.fedoraproject.org/koji/taskinfo?taskID=32368521


For details on the mass rebuild see:

https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
Please fix bfast 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,
bfast will be orphaned. Before branching of Fedora 31,
bfast will be retired, if it still fails to build.

For more details on the FTBFS policy, please visit:
https://fedoraproject.org/wiki/Fails_to_build_from_source

Comment 1 Fedora Release Engineering 2019-02-11 16:53:00 UTC
Created attachment 1529375 [details]
build.log

file build.log too big, will only attach last 1024 bytes

Comment 2 Fedora Release Engineering 2019-02-11 16:53:01 UTC
Created attachment 1529376 [details]
root.log

file root.log too big, will only attach last 1024 bytes

Comment 3 Fedora Release Engineering 2019-02-11 16:53:02 UTC
Created attachment 1529377 [details]
state.log

Comment 4 Fedora Release Engineering 2019-04-26 23:25:02 UTC
Dear Maintainer,

your package has not been built successfully in f30. Action is required from you.

If you can fix your package to build, perform a build in koji, and either create
an update in bodhi, or close this bug without creating an update, if updating is
not appropriate [1]. If you are working on a fix, set the status to ASSIGNED to
acknowledge this. Following the latest policy for such packages [2], your package
can be orphaned if this bug remains in NEW state more than 8 weeks.

[1] https://fedoraproject.org/wiki/Updates_Policy
[2] https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/

Comment 5 Fedora Release Engineering 2019-06-03 21:41:29 UTC
Dear Maintainer,

your package has not been built successfully in f30. Action is required from you.

If you can fix your package to build, perform a build in koji, and either create
an update in bodhi, or close this bug without creating an update, if updating is
not appropriate [1]. If you are working on a fix, set the status to ASSIGNED to
acknowledge this. Following the latest policy for such packages [2], your package
can be orphaned if this bug remains in NEW state more than 8 weeks.

[1] https://fedoraproject.org/wiki/Updates_Policy
[2] https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/

Comment 6 Fedora Release Engineering 2019-06-17 20:41:36 UTC
Dear Maintainer,

your package has not been built successfully in f30. Action is required from you.

If you can fix your package to build, perform a build in koji, and either create
an update in bodhi, or close this bug without creating an update, if updating is
not appropriate [1]. If you are working on a fix, set the status to ASSIGNED to
acknowledge this. Following the latest policy for such packages [2], your package
can be orphaned if this bug remains in NEW state more than 8 weeks.

[1] https://fedoraproject.org/wiki/Updates_Policy
[2] https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/

Comment 7 Petr Pisar 2019-06-20 13:53:10 UTC
gcc  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fgnu89-inline  -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lpthread -o bevalsim ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGRanges.o ../bfast/RGMatches.o ../bfast/RGMatch.o ../bfast/AlignedRead.o ../bfast/AlignedEnd.o ../bfast/AlignedEntry.o bevalsim.o  -lm  -lbz2 -lz
BUILDSTDERR: gcc  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fgnu89-inline  -Wl,-z,relro -Wl,--as-needed  -Wl/usr/bin/ld: ../bfast/RGIndex.o: in function `RGIndexSort':
BUILDSTDERR: /builddir/build/BUILD/bfast-0.7.0a/butil/../bfast/RGIndex.c:784: undefined reference to `pthread_create'
BUILDSTDERR: /usr/bin/ld: /builddir/build/BUILD/bfast-0.7.0a/butil/../bfast/RGIndex.c:796: undefined reference to `pthread_join'
BUILDSTDERR: /usr/bin/ld: /builddir/build/BUILD/bfast-0.7.0a/butil/../bfast/RGIndex.c:857: undefined reference to `pthread_create'
BUILDSTDERR: /usr/bin/ld: /builddir/build/BUILD/bfast-0.7.0a/butil/../bfast/RGIndex.c:869: undefined reference to `pthread_join'
BUILDSTDERR: collect2: error: ld returned 1 exit status

Comment 8 Fedora Release Engineering 2019-07-02 11:13:06 UTC
Dear Maintainer,

your package has not been built successfully in 30. Action is required from you.

If you can fix your package to build, perform a build in koji, and either create
an update in bodhi, or close this bug without creating an update, if updating is
not appropriate [1]. If you are working on a fix, set the status to ASSIGNED to
acknowledge this. Following the latest policy for such packages [2], your package
can be orphaned if this bug remains in NEW state more than 8 weeks.

A week before the mass branching of Fedora 31 according to the schedule [3],
any packages which still have open FTBFS bugs from Fedora 30 will be retired.

[1] https://fedoraproject.org/wiki/Updates_Policy
[2] https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/
[3] https://fedoraproject.org/wiki/Releases/31/Schedule

Comment 9 Fedora Release Engineering 2019-07-02 13:29:28 UTC
Dear Maintainer,

your package has not been built successfully in 30. Action is required from you.

If you can fix your package to build, perform a build in koji, and either create
an update in bodhi, or close this bug without creating an update, if updating is
not appropriate [1]. If you are working on a fix, set the status to ASSIGNED to
acknowledge this. Following the latest policy for such packages [2], your package
can be orphaned if this bug remains in NEW state more than 8 weeks.

A week before the mass branching of Fedora 31 according to the schedule [3],
any packages which still have open FTBFS bugs from Fedora 30 will be retired.

[1] https://fedoraproject.org/wiki/Updates_Policy
[2] https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/
[3] https://fedoraproject.org/wiki/Releases/31/Schedule

Comment 10 Fedora Update System 2019-07-15 14:29:51 UTC
FEDORA-2019-dd697e349b has been submitted as an update to Fedora 30. https://bodhi.fedoraproject.org/updates/FEDORA-2019-dd697e349b

Comment 11 Fedora Update System 2019-07-16 00:54:20 UTC
bfast-0.7.0a-21.fc30 has been pushed to the Fedora 30 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2019-dd697e349b

Comment 12 Fedora Update System 2019-07-24 00:58:26 UTC
bfast-0.7.0a-21.fc30 has been pushed to the Fedora 30 stable repository. If problems still persist, please make note of it in this bug report.

Comment 13 Red Hat Bugzilla 2023-09-14 04:46:46 UTC
The needinfo request[s] on this closed bug have been removed as they have been unresolved for 1000 days